This code is available at https://github.com/aaronsk7/guppy-methylation

https://cran.r-project.org/web/packages/RCircos/vignettes/Using_RCircos.pdf

dmrs before annotation

library(GenomicFeatures)
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## Loading required package: AnnotationDbi
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## Welcome to Bioconductor
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##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
library(BiocManager)
library(RCircos)
library(dplyr)
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## Attaching package: 'dplyr'
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##     intersect, setdiff, setequal, union
library(data.table)
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## Attaching package: 'data.table'
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## The following object is masked from 'package:IRanges':
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##     shift
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##     first, second
dmrseqCvG <- readRDS("/mnt/data/aaron/projects/guppy-methylation/dmrseqrds/dmrseqCvG.rds")
dmrseqCvL <- readRDS("/mnt/data/aaron/projects/guppy-methylation/dmrseqrds/dmrseqCvL.rds")
dmrseqGvL <- readRDS("/mnt/data/aaron/projects/guppy-methylation/dmrseqrds/dmrseqGvL.rds")
dmrseqCvG
## GRanges object with 110780 ranges and 7 metadata columns:
##              seqnames            ranges strand |         L      area
##                 <Rle>         <IRanges>  <Rle> | <integer> <numeric>
##        [1]       LG21 15968848-15969922      * |        69  15.17042
##        [2]       LG13 18160946-18161700      * |        75  17.10434
##        [3]        LG8 27368425-27368499      * |        22   1.10760
##        [4] KK215287.1     628700-629071      * |        42   2.46231
##        [5] KK215308.1       92510-92874      * |        65   4.00345
##        ...        ...               ...    ... .       ...       ...
##   [110776]       LG23   9878111-9878189      * |         5  0.325355
##   [110777]        LG4 23297854-23297875      * |         5  0.255117
##   [110778]        LG7 27950078-27950229      * |         6  0.313935
##   [110779]        LG5   6841358-6841438      * |        10  0.530287
##   [110780]       LG11 26442624-26442768      * |         5  0.269579
##                    beta         stat        pval      qval             index
##               <numeric>    <numeric>   <numeric> <numeric>         <IRanges>
##        [1]    -0.512678     -12.8289 3.16845e-05  0.719377 11675769-11675837
##        [2]     0.480479      12.3558 4.01337e-05  0.719377   4371608-4371682
##        [3]    -0.359863     -12.3461 4.11898e-05  0.719377 18010981-18011002
##        [4]    -0.357702     -12.2466 4.22460e-05  0.719377     186337-186378
##        [5]    -0.303095     -12.1655 4.43583e-05  0.719377     437886-437950
##        ...          ...          ...         ...       ...               ...
##   [110776] -1.01705e-04 -0.000542256    0.999958  0.999982 12925373-12925377
##   [110777]  6.70295e-05  0.000511830    0.999960  0.999982 14612277-14612281
##   [110778] -3.85822e-05 -0.000399293    0.999964  0.999982 17189367-17189372
##   [110779] -1.24165e-05 -0.000137088    0.999985  0.999989 15004610-15004619
##   [110780] -1.32305e-05 -0.000108119    0.999989  0.999989   3196546-3196550
##   -------
##   seqinfo: 1181 sequences from an unspecified genome; no seqlengths
head(dmrseqCvL)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG19 10333007-10333692      * |        71  16.55967  0.576766
##   [2]       LG21 14273013-14273749      * |        81  14.61418  0.464748
##   [3] KK215293.1     186354-186845      * |        61   5.16072  0.391140
##   [4]       LG13 22015858-22016352      * |        82  14.22619  0.439795
##   [5] KK215283.1   1376211-1376895      * |       104  13.72310  0.361397
##   [6]       LG17   1251474-1251938      * |        61  12.56082 -0.401292
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]   18.9921 9.99999e-07  0.111437   8673138-8673208
##   [2]   15.3892 7.99999e-06  0.445748 11372899-11372979
##   [3]   12.1651 4.00000e-05  0.910330     296821-296881
##   [4]   11.5744 6.59999e-05  0.910330   4374338-4374419
##   [5]   11.5460 6.59999e-05  0.910330       56943-57046
##   [6]  -11.4403 7.09999e-05  0.910330   7069344-7069404
##   -------
##   seqinfo: 1180 sequences from an unspecified genome; no seqlengths
head(dmrseqGvL)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG11 28461237-28461741      * |       108  11.63697 -0.277374
##   [2] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [3]       LG20 17269425-17270374      * |        73  10.41376  0.475571
##   [4]        LG1 22240537-22241922      * |        78   8.68085  0.351599
##   [5]        LG2 28494008-28495445      * |        65   9.70966  0.462682
##   [6]       LG13 18160946-18161831      * |        95  16.31186 -0.397064
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]  -16.2750 7.14404e-06  0.653851   3678849-3678956
##   [2]   15.2345 1.78601e-05  0.749204       65611-65766
##   [3]   14.5876 2.50041e-05  0.749204 12375529-12375601
##   [4]   13.2709 4.64363e-05  0.749204   1550715-1550792
##   [5]   12.8543 5.47710e-05  0.749204 11413014-11413078
##   [6]  -12.7574 5.59616e-05  0.749204   4929871-4929965
##   -------
##   seqinfo: 1169 sequences from an unspecified genome; no seqlengths
CvGdmrs <- as.data.frame(dmrseqCvG,row.names = 1:nrow(as.data.frame(ranges(dmrseqCvG))))
head(CvGdmrs,10)
##      seqnames    start      end width strand  L      area       beta      stat
## 1        LG21 15968848 15969922  1075      * 69 15.170417 -0.5126778 -12.82890
## 2        LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 3         LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 4  KK215287.1   628700   629071   372      * 42  2.462310 -0.3577019 -12.24660
## 5  KK215308.1    92510    92874   365      * 65  4.003455 -0.3030945 -12.16552
## 6         LG2 18092802 18093635   834      * 53  9.373725 -0.3978501 -12.07243
## 7         LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8  KK215283.1   934758   935340   583      * 78  5.694514  0.3357201  11.28039
## 9        LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
## 10       LG13 18052556 18054100  1545      * 81 10.961955 -0.3413481 -11.11704
##            pval      qval index.start index.end index.width
## 1  3.168447e-05 0.7193775    11675769  11675837          69
## 2  4.013367e-05 0.7193775     4371608   4371682          75
## 3  4.118982e-05 0.7193775    18010981  18011002          22
## 4  4.224596e-05 0.7193775      186337    186378          42
## 5  4.435826e-05 0.7193775      437886    437950          65
## 6  4.541441e-05 0.7193775     9863892   9863944          53
## 7  6.442510e-05 0.7193775    14903599  14903659          61
## 8  8.449193e-05 0.7193775       37410     37487          78
## 9  9.082882e-05 0.7193775     2481310   2481355          46
## 10 9.399727e-05 0.7193775     4367383   4367463          81
CvLdmrs <- as.data.frame(dmrseqCvL,row.names = 1:nrow(as.data.frame(ranges(dmrseqCvL))))
head(CvLdmrs,10)
##      seqnames    start      end width strand   L      area       beta      stat
## 1        LG19 10333007 10333692   686      *  71 16.559670  0.5767663  18.99209
## 2        LG21 14273013 14273749   737      *  81 14.614182  0.4647484  15.38915
## 3  KK215293.1   186354   186845   492      *  61  5.160722  0.3911403  12.16515
## 4        LG13 22015858 22016352   495      *  82 14.226193  0.4397952  11.57442
## 5  KK215283.1  1376211  1376895   685      * 104 13.723096  0.3613973  11.54604
## 6        LG17  1251474  1251938   465      *  61 12.560822 -0.4012925 -11.44033
## 7         LG8 18982718 18983377   660      *  60  7.212046 -0.3746378 -11.38354
## 8        LG11 14181818 14182182   365      *  58  4.745863 -0.3570840 -11.25378
## 9         LG2 16355666 16355981   316      *  76  6.324347  0.3183476  10.87880
## 10        LG4 15409098 15410303  1206      *  85 11.219454 -0.3823658 -10.81088
##            pval      qval index.start index.end index.width
## 1  9.999990e-07 0.1114369     8673138   8673208          71
## 2  7.999992e-06 0.4457476    11372899  11372979          81
## 3  3.999996e-05 0.9103295      296821    296881          61
## 4  6.599993e-05 0.9103295     4374338   4374419          82
## 5  6.599993e-05 0.9103295       56943     57046         104
## 6  7.099993e-05 0.9103295     7069344   7069404          61
## 7  7.399993e-05 0.9103295    17405986  17406045          60
## 8  8.099992e-05 0.9103295     2836015   2836072          58
## 9  1.009999e-04 0.9103295     9599998   9600073          76
## 10 1.069999e-04 0.9103295    14042960  14043044          85
GvLdmrs <- as.data.frame(dmrseqGvL,row.names = 1:nrow(as.data.frame(ranges(dmrseqGvL))))
head(GvLdmrs,10)
##      seqnames    start      end width strand   L      area       beta      stat
## 1        LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 2  KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 3        LG20 17269425 17270374   950      *  73 10.413759  0.4755714  14.58765
## 4         LG1 22240537 22241922  1386      *  78  8.680847  0.3515985  13.27092
## 5         LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 6        LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7  KK215287.1   944627   944828   202      *  36  4.299457 -0.4584372 -12.68316
## 8        LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9  KK215306.1   101373   102087   715      *  68  9.626653  0.4324903  12.37528
## 10        LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##            pval      qval index.start index.end index.width
## 1  7.144039e-06 0.6538511     3678849   3678956         108
## 2  1.786010e-05 0.7492043       65611     65766         156
## 3  2.500414e-05 0.7492043    12375529  12375601          73
## 4  4.643626e-05 0.7492043     1550715   1550792          78
## 5  5.477097e-05 0.7492043    11413014  11413078          65
## 6  5.596164e-05 0.7492043     4929871   4929965          95
## 7  6.072433e-05 0.7492043      223719    223754          36
## 8  6.548703e-05 0.7492043     3123427   3123501          75
## 9  7.620309e-05 0.7749346      479142    479209          68
## 10 9.287251e-05 0.7879743    16775120  16775177          58
gtf <- rtracklayer::import("/mnt/data/aaron/projects/guppy-methylation/Poecilia_reticulata.Guppy_female_1.0_MT.103.gtf")
head(gtf)
## GRanges object with 6 ranges and 21 metadata columns:
##       seqnames    ranges strand |   source        type     score     phase
##          <Rle> <IRanges>  <Rle> | <factor>    <factor> <numeric> <integer>
##   [1]      LG2  813-1286      - |  ensembl gene               NA      <NA>
##   [2]      LG2  813-1286      - |  ensembl transcript         NA      <NA>
##   [3]      LG2  813-1286      - |  ensembl exon               NA      <NA>
##   [4]      LG2  816-1286      - |  ensembl CDS                NA         0
##   [5]      LG2 1284-1286      - |  ensembl start_codon        NA         0
##   [6]      LG2   813-815      - |  ensembl stop_codon         NA         0
##                  gene_id gene_version gene_source   gene_biotype
##              <character>  <character> <character>    <character>
##   [1] ENSPREG00000006268            1     ensembl protein_coding
##   [2] ENSPREG00000006268            1     ensembl protein_coding
##   [3] ENSPREG00000006268            1     ensembl protein_coding
##   [4] ENSPREG00000006268            1     ensembl protein_coding
##   [5] ENSPREG00000006268            1     ensembl protein_coding
##   [6] ENSPREG00000006268            1     ensembl protein_coding
##            transcript_id transcript_version transcript_source
##              <character>        <character>       <character>
##   [1]               <NA>               <NA>              <NA>
##   [2] ENSPRET00000009285                  1           ensembl
##   [3] ENSPRET00000009285                  1           ensembl
##   [4] ENSPRET00000009285                  1           ensembl
##   [5] ENSPRET00000009285                  1           ensembl
##   [6] ENSPRET00000009285                  1           ensembl
##       transcript_biotype exon_number            exon_id exon_version
##              <character> <character>        <character>  <character>
##   [1]               <NA>        <NA>               <NA>         <NA>
##   [2]     protein_coding        <NA>               <NA>         <NA>
##   [3]     protein_coding           1 ENSPREE00000064246            1
##   [4]     protein_coding           1               <NA>         <NA>
##   [5]     protein_coding           1               <NA>         <NA>
##   [6]     protein_coding           1               <NA>         <NA>
##               protein_id protein_version   gene_name transcript_name
##              <character>     <character> <character>     <character>
##   [1]               <NA>            <NA>        <NA>            <NA>
##   [2]               <NA>            <NA>        <NA>            <NA>
##   [3]               <NA>            <NA>        <NA>            <NA>
##   [4] ENSPREP00000009175               1        <NA>            <NA>
##   [5]               <NA>            <NA>        <NA>            <NA>
##   [6]               <NA>            <NA>        <NA>            <NA>
##       projection_parent_gene projection_parent_transcript
##                  <character>                  <character>
##   [1]                   <NA>                         <NA>
##   [2]                   <NA>                         <NA>
##   [3]                   <NA>                         <NA>
##   [4]                   <NA>                         <NA>
##   [5]                   <NA>                         <NA>
##   [6]                   <NA>                         <NA>
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
my_genes <- gtf[gtf$type == "gene"]
head(my_genes)
## GRanges object with 6 ranges and 21 metadata columns:
##       seqnames        ranges strand |   source     type     score     phase
##          <Rle>     <IRanges>  <Rle> | <factor> <factor> <numeric> <integer>
##   [1]      LG2      813-1286      - |  ensembl     gene        NA      <NA>
##   [2]      LG2   18959-21569      - |  ensembl     gene        NA      <NA>
##   [3]      LG2   30025-35085      + |  ensembl     gene        NA      <NA>
##   [4]      LG2 306358-537092      + |  ensembl     gene        NA      <NA>
##   [5]      LG2 621822-632265      + |  ensembl     gene        NA      <NA>
##   [6]      LG2 627410-629578      - |  ensembl     gene        NA      <NA>
##                  gene_id gene_version gene_source   gene_biotype transcript_id
##              <character>  <character> <character>    <character>   <character>
##   [1] ENSPREG00000006268            1     ensembl protein_coding          <NA>
##   [2] ENSPREG00000006273            1     ensembl protein_coding          <NA>
##   [3] ENSPREG00000006291            1     ensembl protein_coding          <NA>
##   [4] ENSPREG00000006354            1     ensembl protein_coding          <NA>
##   [5] ENSPREG00000006412            1     ensembl protein_coding          <NA>
##   [6] ENSPREG00000006451            1     ensembl protein_coding          <NA>
##       transcript_version transcript_source transcript_biotype exon_number
##              <character>       <character>        <character> <character>
##   [1]               <NA>              <NA>               <NA>        <NA>
##   [2]               <NA>              <NA>               <NA>        <NA>
##   [3]               <NA>              <NA>               <NA>        <NA>
##   [4]               <NA>              <NA>               <NA>        <NA>
##   [5]               <NA>              <NA>               <NA>        <NA>
##   [6]               <NA>              <NA>               <NA>        <NA>
##           exon_id exon_version  protein_id protein_version   gene_name
##       <character>  <character> <character>     <character> <character>
##   [1]        <NA>         <NA>        <NA>            <NA>        <NA>
##   [2]        <NA>         <NA>        <NA>            <NA>        <NA>
##   [3]        <NA>         <NA>        <NA>            <NA>      arl13b
##   [4]        <NA>         <NA>        <NA>            <NA>  zgc:152904
##   [5]        <NA>         <NA>        <NA>            <NA>        gart
##   [6]        <NA>         <NA>        <NA>            <NA>      n6amt1
##       transcript_name projection_parent_gene projection_parent_transcript
##           <character>            <character>                  <character>
##   [1]            <NA>                   <NA>                         <NA>
##   [2]            <NA>                   <NA>                         <NA>
##   [3]            <NA>                   <NA>                         <NA>
##   [4]            <NA>                   <NA>                         <NA>
##   [5]            <NA>                   <NA>                         <NA>
##   [6]            <NA>                   <NA>                         <NA>
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
mcols(my_genes) <- mcols(my_genes)[c(5,8,18)]
head(my_genes)
## GRanges object with 6 ranges and 3 metadata columns:
##       seqnames        ranges strand |            gene_id   gene_biotype
##          <Rle>     <IRanges>  <Rle> |        <character>    <character>
##   [1]      LG2      813-1286      - | ENSPREG00000006268 protein_coding
##   [2]      LG2   18959-21569      - | ENSPREG00000006273 protein_coding
##   [3]      LG2   30025-35085      + | ENSPREG00000006291 protein_coding
##   [4]      LG2 306358-537092      + | ENSPREG00000006354 protein_coding
##   [5]      LG2 621822-632265      + | ENSPREG00000006412 protein_coding
##   [6]      LG2 627410-629578      - | ENSPREG00000006451 protein_coding
##         gene_name
##       <character>
##   [1]        <NA>
##   [2]        <NA>
##   [3]      arl13b
##   [4]  zgc:152904
##   [5]        gart
##   [6]      n6amt1
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
gff <- rtracklayer::import("/mnt/data/aaron/projects/guppy-methylation/Poecilia_reticulata.Guppy_female_1.0_MT.dna_sm.toplevel_out.gff")
head(gff)
## GRanges object with 6 ranges and 5 metadata columns:
##       seqnames      ranges strand |   source             type     score
##          <Rle>   <IRanges>  <Rle> | <factor>         <factor> <numeric>
##   [1]      LG1   6715-6924      + |  cpgplot sequence_feature        NA
##   [2]      LG1   8186-8489      + |  cpgplot sequence_feature        NA
##   [3]      LG1 12358-12761      + |  cpgplot sequence_feature        NA
##   [4]      LG1 29724-30103      + |  cpgplot sequence_feature        NA
##   [5]      LG1 45593-45901      + |  cpgplot sequence_feature        NA
##   [6]      LG1 50080-50390      + |  cpgplot sequence_feature        NA
##           phase          ID
##       <integer> <character>
##   [1]      <NA>       LG1.1
##   [2]      <NA>       LG1.2
##   [3]      <NA>       LG1.3
##   [4]      <NA>       LG1.4
##   [5]      <NA>       LG1.5
##   [6]      <NA>       LG1.6
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
my_CpGislands <- gff[gff$type == "sequence_feature"]
head(my_CpGislands)
## GRanges object with 6 ranges and 5 metadata columns:
##       seqnames      ranges strand |   source             type     score
##          <Rle>   <IRanges>  <Rle> | <factor>         <factor> <numeric>
##   [1]      LG1   6715-6924      + |  cpgplot sequence_feature        NA
##   [2]      LG1   8186-8489      + |  cpgplot sequence_feature        NA
##   [3]      LG1 12358-12761      + |  cpgplot sequence_feature        NA
##   [4]      LG1 29724-30103      + |  cpgplot sequence_feature        NA
##   [5]      LG1 45593-45901      + |  cpgplot sequence_feature        NA
##   [6]      LG1 50080-50390      + |  cpgplot sequence_feature        NA
##           phase          ID
##       <integer> <character>
##   [1]      <NA>       LG1.1
##   [2]      <NA>       LG1.2
##   [3]      <NA>       LG1.3
##   [4]      <NA>       LG1.4
##   [5]      <NA>       LG1.5
##   [6]      <NA>       LG1.6
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
mcols(my_CpGislands) <- mcols(my_CpGislands)[c(1,5)]
head(my_CpGislands)
## GRanges object with 6 ranges and 2 metadata columns:
##       seqnames      ranges strand |   source          ID
##          <Rle>   <IRanges>  <Rle> | <factor> <character>
##   [1]      LG1   6715-6924      + |  cpgplot       LG1.1
##   [2]      LG1   8186-8489      + |  cpgplot       LG1.2
##   [3]      LG1 12358-12761      + |  cpgplot       LG1.3
##   [4]      LG1 29724-30103      + |  cpgplot       LG1.4
##   [5]      LG1 45593-45901      + |  cpgplot       LG1.5
##   [6]      LG1 50080-50390      + |  cpgplot       LG1.6
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
my_Promotersdf <- read.table("/mnt/data/aaron/projects/guppy-methylation/Poecilia_reticulata.Guppy_female_1.0_MT.103_tss.bed",header = FALSE,stringsAsFactors=FALSE)
head(my_Promotersdf)
##    V1     V2     V3 V4                 V5                 V6         V7
## 1 LG2  28525  31526  + ENSPREG00000006291 ENSPRET00000009322     arl13b
## 2 LG2 304858 307859  + ENSPREG00000006354 ENSPRET00000009453 zgc:152904
## 3 LG2 446170 449171  + ENSPREG00000006354 ENSPRET00000009478 zgc:152904
## 4 LG2 446848 449849  + ENSPREG00000006354 ENSPRET00000009478 zgc:152904
## 5 LG2 620322 623323  + ENSPREG00000006412 ENSPRET00000009554       gart
## 6 LG2 620942 623943  + ENSPREG00000006412 ENSPRET00000009572       gart
my_Promoters <- makeGRangesFromDataFrame(my_Promotersdf,
                         keep.extra.columns=TRUE,
                         ignore.strand=FALSE,
                         seqinfo=NULL,
                         seqnames.field=c("V1"),
                         start.field="V2",
                         end.field=c("V3"),
                         strand.field="V4",
                         starts.in.df.are.0based=FALSE)

head(my_Promoters)
## GRanges object with 6 ranges and 3 metadata columns:
##       seqnames        ranges strand |                 V5                 V6
##          <Rle>     <IRanges>  <Rle> |        <character>        <character>
##   [1]      LG2   28525-31526      + | ENSPREG00000006291 ENSPRET00000009322
##   [2]      LG2 304858-307859      + | ENSPREG00000006354 ENSPRET00000009453
##   [3]      LG2 446170-449171      + | ENSPREG00000006354 ENSPRET00000009478
##   [4]      LG2 446848-449849      + | ENSPREG00000006354 ENSPRET00000009478
##   [5]      LG2 620322-623323      + | ENSPREG00000006412 ENSPRET00000009554
##   [6]      LG2 620942-623943      + | ENSPREG00000006412 ENSPRET00000009572
##                V7
##       <character>
##   [1]      arl13b
##   [2]  zgc:152904
##   [3]  zgc:152904
##   [4]  zgc:152904
##   [5]        gart
##   [6]        gart
##   -------
##   seqinfo: 452 sequences from an unspecified genome; no seqlengths

dmrs annotated to genes

ol1 <- findOverlaps(dmrseqCvG,my_genes)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215341.1, KK215360.1, KK215378.1, KK215383.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215415.1, KK215418.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215440.1, KK215441.1, KK215443.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215454.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215472.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215501.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215547.1, KK215548.1, KK215549.1, KK215551.1, KK215556.1, KK215558.1, KK215559.1, KK215560.1, KK215561.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215581.1, KK215583.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215589.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215620.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215627.1, KK215628.1, KK215629.1, KK215630.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215639.1, KK215641.1, KK215642.1, KK215645.1, KK215646.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215664.1, KK215665.1, KK215668.1, KK215669.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215683.1, KK215684.1, KK215688.1, KK215692.1, KK215695.1, KK215700.1, KK215701.1, KK215703.1, KK215704.1, KK215705.1, KK215706.1, KK215709.1, KK215710.1, KK215711.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215724.1, KK215726.1, KK215727.1, KK215728.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215741.1, KK215742.1, KK215743.1, KK215745.1, KK215750.1, KK215752.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215762.1, KK215763.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215779.1, KK215780.1, KK215782.1, KK215783.1, KK215785.1, KK215786.1, KK215788.1, KK215789.1, KK215792.1, KK215794.1, KK215795.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215815.1, KK215816.1, KK215821.1, KK215825.1, KK215827.1, KK215832.1, KK215834.1, KK215836.1, KK215837.1, KK215838.1, KK215843.1, KK215848.1, KK215849.1, KK215854.1, KK215857.1, KK215858.1, KK215859.1, KK215861.1, KK215863.1, KK215864.1, KK215872.1, KK215873.1, KK215875.1, KK215877.1, KK215878.1, KK215880.1, KK215881.1, KK215882.1, KK215885.1, KK215886.1, KK215890.1, KK215891.1, KK215894.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215907.1, KK215909.1, KK215910.1, KK215911.1, KK215914.1, KK215915.1, KK215918.1, KK215921.1, KK215922.1, KK215923.1, KK215928.1, KK215929.1, KK215934.1, KK215935.1, KK215937.1, KK215942.1, KK215943.1, KK215945.1, KK215946.1, KK215949.1, KK215951.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215962.1, KK215965.1, KK215967.1, KK215969.1, KK215970.1, KK215973.1, KK215974.1, KK215976.1, KK215977.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215990.1, KK215993.1, KK215994.1, KK215997.1, KK215999.1, KK216000.1, KK216001.1, KK216012.1, KK216015.1, KK216017.1, KK216018.1, KK216021.1, KK216023.1, KK216025.1, KK216026.1, KK216028.1, KK216029.1, KK216030.1, KK216032.1, KK216033.1, KK216034.1, KK216035.1, KK216037.1, KK216038.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216049.1, KK216053.1, KK216063.1, KK216064.1, KK216065.1, KK216066.1, KK216067.1, KK216068.1, KK216069.1, KK216070.1, KK216071.1, KK216072.1, KK216074.1, KK216075.1, KK216076.1, KK216079.1, KK216082.1, KK216084.1, KK216085.1, KK216086.1, KK216089.1, KK216093.1, KK216094.1, KK216097.1, KK216099.1, KK216102.1, KK216103.1, KK216109.1, KK216111.1, KK216114.1, KK216118.1, KK216120.1, KK216122.1, KK216124.1, KK216128.1, KK216133.1, KK216134.1, KK216135.1, KK216141.1, KK216142.1, KK216143.1, KK216150.1, KK216152.1, KK216155.1, KK216157.1, KK216158.1, KK216165.1, KK216166.1, KK216169.1, KK216171.1, KK216172.1, KK216173.1, KK216174.1, KK216175.1, KK216177.1, KK216180.1, KK216184.1, KK216186.1, KK216190.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216200.1, KK216203.1, KK216208.1, KK216212.1, KK216213.1, KK216215.1, KK216219.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216229.1, KK216232.1, KK216236.1, KK216237.1, KK216238.1, KK216240.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216259.1, KK216260.1, KK216261.1, KK216264.1, KK216266.1, KK216270.1, KK216273.1, KK216275.1, KK216278.1, KK216280.1, KK216281.1, KK216282.1, KK216284.1, KK216285.1, KK216287.1, KK216289.1, KK216290.1, KK216295.1, KK216303.1, KK216306.1, KK216310.1, KK216313.1, KK216320.1, KK216322.1, KK216323.1, KK216324.1, KK216325.1, KK216326.1, KK216329.1, KK216330.1, KK216331.1, KK216334.1, KK216336.1, KK216341.1, KK216342.1, KK216351.1, KK216359.1, KK216360.1, KK216363.1, KK216364.1, KK216366.1, KK216368.1, KK216370.1, KK216371.1, KK216377.1, KK216383.1, KK216384.1, KK216389.1, KK216391.1, KK216394.1, KK216396.1, KK216402.1, KK216404.1, KK216405.1, KK216408.1, KK216410.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216423.1, KK216428.1, KK216432.1, KK216433.1, KK216436.1, KK216438.1, KK216440.1, KK216442.1, KK216445.1, KK216447.1, KK216451.1, KK216452.1, KK216453.1, KK216456.1, KK216457.1, KK216458.1, KK216462.1, KK216468.1, KK216477.1, KK216482.1, KK216492.1, KK216502.1, KK216504.1, KK216506.1, KK216507.1, KK216508.1, KK216510.1, KK216511.1, KK216512.1, KK216513.1, KK216514.1, KK216515.1, KK216519.1, KK216523.1, KK216526.1, KK216530.1, KK216531.1, KK216538.1, KK216540.1, KK216548.1, KK216552.1, KK216553.1, KK216556.1, KK216569.1, KK216571.1, KK216572.1, KK216574.1, KK216576.1, KK216592.1, KK216599.1, KK216606.1, KK216607.1, KK216610.1, KK216615.1, KK216627.1, KK216638.1, KK216640.1, KK216647.1, KK216651.1, KK216657.1, KK216661.1, KK216665.1, KK216672.1, KK216674.1, KK216678.1, KK216680.1, KK216685.1, KK216691.1, KK216695.1, KK216709.1, KK216712.1, KK216714.1, KK216716.1, KK216717.1, KK216725.1, KK216726.1, KK216732.1, KK216737.1, KK216740.1, KK216745.1, KK216746.1, KK216748.1, KK216752.1, KK216758.1, KK216763.1, KK216773.1, KK216779.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216800.1, KK216804.1, KK216811.1, KK216814.1, KK216815.1, KK216817.1, KK216830.1, KK216831.1, KK216834.1, KK216842.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216863.1, KK216865.1, KK216867.1, KK216870.1, KK216873.1, KK216879.1, KK216881.1, KK216887.1, KK216896.1, KK216898.1, KK216899.1, KK216903.1, KK216905.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216922.1, KK216923.1, KK216930.1, KK216931.1, KK216934.1, KK216942.1, KK216943.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216963.1, KK216964.1, KK216965.1, KK216968.1, KK216971.1, KK216973.1, KK216974.1, KK216975.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216999.1, KK217000.1, KK217001.1, KK217002.1, KK217003.1, KK217007.1, KK217012.1, KK217019.1, KK217032.1, KK217037.1, KK217059.1, KK217063.1, KK217065.1, KK217066.1, KK217072.1, KK217074.1, KK217076.1, KK217077.1, KK217079.1, KK217082.1, KK217083.1, KK217086.1, KK217088.1, KK217093.1, KK217098.1, KK217101.1, KK217103.1, KK217105.1, KK217109.1, KK217111.1, KK217112.1, KK217114.1, KK217117.1, KK217119.1, KK217120.1, KK217121.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217135.1, KK217140.1, KK217146.1, KK217147.1, KK217182.
ol1
## Hits object with 56579 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         2        6028
##       [2]         3       17487
##       [3]         3       17488
##       [4]         4       22168
##       [5]         7        4577
##       ...       ...         ...
##   [56575]    110773       21103
##   [56576]    110775        7760
##   [56577]    110776       21716
##   [56578]    110777       10297
##   [56579]    110779        4735
##   -------
##   queryLength: 110780 / subjectLength: 23254
CvGgenes <- dmrseqCvG[queryHits(ol1)]
mygenesol1 <- my_genes[subjectHits(ol1)]
head(CvGgenes)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG13 18160946-18161700      * |        75  17.10434  0.480479
##   [2]        LG8 27368425-27368499      * |        22   1.10760 -0.359863
##   [3]        LG8 27368425-27368499      * |        22   1.10760 -0.359863
##   [4] KK215287.1     628700-629071      * |        42   2.46231 -0.357702
##   [5]        LG5   2971274-2971545      * |        61   8.49567  0.378574
##   [6]        LG5   2971274-2971545      * |        61   8.49567  0.378574
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]   12.3558 4.01337e-05  0.719377   4371608-4371682
##   [2]  -12.3461 4.11898e-05  0.719377 18010981-18011002
##   [3]  -12.3461 4.11898e-05  0.719377 18010981-18011002
##   [4]  -12.2466 4.22460e-05  0.719377     186337-186378
##   [5]   11.6533 6.44251e-05  0.719377 14903599-14903659
##   [6]   11.6533 6.44251e-05  0.719377 14903599-14903659
##   -------
##   seqinfo: 1181 sequences from an unspecified genome; no seqlengths
mygenesol1
## GRanges object with 56579 ranges and 3 metadata columns:
##             seqnames            ranges strand |            gene_id
##                <Rle>         <IRanges>  <Rle> |        <character>
##       [1]       LG13 18160798-18170662      - | ENSPREG00000001265
##       [2]        LG8 27350463-27375917      - | ENSPREG00000012374
##       [3]        LG8 27361755-27370706      - | ENSPREG00000012413
##       [4] KK215287.1     624615-641867      - | ENSPREG00000006712
##       [5]        LG5   2895024-3016337      + | ENSPREG00000022808
##       ...        ...               ...    ... .                ...
##   [56575]       LG18 11954586-12063344      - | ENSPREG00000015063
##   [56576]       LG10   4384736-4654413      + | ENSPREG00000021348
##   [56577]       LG23   9858311-9900905      + | ENSPREG00000009690
##   [56578]        LG4 23260611-23303354      + | ENSPREG00000008408
##   [56579]        LG5   6823071-6850398      + | ENSPREG00000006274
##             gene_biotype   gene_name
##              <character> <character>
##       [1] protein_coding        <NA>
##       [2] protein_coding       btr30
##       [3] protein_coding        <NA>
##       [4] protein_coding      supt5h
##       [5] protein_coding        <NA>
##       ...            ...         ...
##   [56575] protein_coding      efnb3b
##   [56576] protein_coding       TENM1
##   [56577] protein_coding     ahcyl2b
##   [56578] protein_coding      unc13a
##   [56579] protein_coding      iffo2b
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
CvGgenesdf <- as.data.frame(CvGgenes,row.names = 1:nrow(as.data.frame(ranges(CvGgenes))))
str(CvGgenesdf)
## 'data.frame':    56579 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1181 levels "KK215283.1","KK215284.1",..: 1163 1180 1180 5 1177 1177 1 1160 1163 1169 ...
##  $ start      : int  18160946 27368425 27368425 628700 2971274 2971274 934758 32171882 18052556 10333007 ...
##  $ end        : int  18161700 27368499 27368499 629071 2971545 2971545 935340 32172301 18054100 10333692 ...
##  $ width      : int  755 75 75 372 272 272 583 420 1545 686 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  75 22 22 42 61 61 78 46 81 70 ...
##  $ area       : num  17.1 1.11 1.11 2.46 8.5 ...
##  $ beta       : num  0.48 -0.36 -0.36 -0.358 0.379 ...
##  $ stat       : num  12.4 -12.3 -12.3 -12.2 11.7 ...
##  $ pval       : num  4.01e-05 4.12e-05 4.12e-05 4.22e-05 6.44e-05 ...
##  $ qval       : num  0.719 0.719 0.719 0.719 0.719 ...
##  $ index.start: int  4371608 18010981 18010981 186337 14903599 14903599 37410 2481310 4367383 8864531 ...
##  $ index.end  : int  4371682 18011002 18011002 186378 14903659 14903659 37487 2481355 4367463 8864600 ...
##  $ index.width: int  75 22 22 42 61 61 78 46 81 70 ...
mygenesoldf1 <- as.data.frame(mygenesol1,row.names = 1:nrow(as.data.frame(ranges(mygenesol1))))
head(mygenesoldf1)
##     seqnames    start      end  width strand            gene_id   gene_biotype
## 1       LG13 18160798 18170662   9865      - ENSPREG00000001265 protein_coding
## 2        LG8 27350463 27375917  25455      - ENSPREG00000012374 protein_coding
## 3        LG8 27361755 27370706   8952      - ENSPREG00000012413 protein_coding
## 4 KK215287.1   624615   641867  17253      - ENSPREG00000006712 protein_coding
## 5        LG5  2895024  3016337 121314      + ENSPREG00000022808 protein_coding
## 6        LG5  2967898  2981871  13974      + ENSPREG00000022867 protein_coding
##   gene_name
## 1      <NA>
## 2     btr30
## 3      <NA>
## 4    supt5h
## 5      <NA>
## 6    asb14a
CvGgenesdf <- cbind(CvGgenesdf,mygenesoldf1[c("gene_id","gene_biotype","gene_name")])
CvGgenesdf$seqnames <- as.character(CvGgenesdf$seqnames)
head(CvGgenesdf)
##     seqnames    start      end width strand  L      area       beta      stat
## 1       LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2        LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 3        LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 4 KK215287.1   628700   629071   372      * 42  2.462310 -0.3577019 -12.24660
## 5        LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 6        LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
##           pval      qval index.start index.end index.width            gene_id
## 1 4.013367e-05 0.7193775     4371608   4371682          75 ENSPREG00000001265
## 2 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012374
## 3 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012413
## 4 4.224596e-05 0.7193775      186337    186378          42 ENSPREG00000006712
## 5 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022808
## 6 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
##     gene_biotype gene_name
## 1 protein_coding      <NA>
## 2 protein_coding     btr30
## 3 protein_coding      <NA>
## 4 protein_coding    supt5h
## 5 protein_coding      <NA>
## 6 protein_coding    asb14a
CvGgeneschrdf <- CvGgenesdf[grep("LG",CvGgenesdf$seqnames),]
head(CvGgeneschrdf,20)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG13 18160946 18161700   755      *  75 17.104340  0.4804793  12.35578
## 2       LG8 27368425 27368499    75      *  22  1.107603 -0.3598625 -12.34614
## 3       LG8 27368425 27368499    75      *  22  1.107603 -0.3598625 -12.34614
## 5       LG5  2971274  2971545   272      *  61  8.495669  0.3785743  11.65333
## 6       LG5  2971274  2971545   272      *  61  8.495669  0.3785743  11.65333
## 8      LG10 32171882 32172301   420      *  46  8.597024  0.4390605  11.17294
## 9      LG13 18052556 18054100  1545      *  81 10.961955 -0.3413481 -11.11704
## 10     LG19 10333007 10333692   686      *  70 10.588759  0.4116465  10.86281
## 11     LG19  8889655  8889899   245      *  47  2.420966 -0.2756728 -10.81171
## 13     LG20 10526898 10527306   409      *  61  5.646018  0.2998656  10.73088
## 14     LG19 25883884 25884226   343      *  27  1.833101 -0.3775782 -10.70954
## 15     LG11  3353555  3354323   769      *  64  7.604367  0.3888157  10.70122
## 16     LG11 10641658 10642177   520      *  56  6.750824  0.4028755  10.69685
## 17      LG4  4685116  4685638   523      *  91 11.170358  0.2888801  10.61794
## 18     LG10 14876068 14876399   332      *  40  6.857049 -0.4594013 -10.43686
## 19      LG1 17896682 17897364   683      *  78  7.067168 -0.4086131 -10.41726
## 20      LG2 43981407 43981496    90      *  17  2.421572 -0.5597475 -10.38898
## 21     LG15 25594055 25594564   510      *  40  5.525193 -0.3638675 -10.28654
## 22     LG22  7737092  7737838   747      *  53  9.508586 -0.3861418 -10.21539
## 23      LG4 20353270 20354327  1058      * 106 14.873154 -0.3722110 -10.15553
##            pval      qval index.start index.end index.width            gene_id
## 1  4.013367e-05 0.7193775     4371608   4371682          75 ENSPREG00000001265
## 2  4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012374
## 3  4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012413
## 5  6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022808
## 6  6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 8  9.082882e-05 0.7193775     2481310   2481355          46 ENSPREG00000011064
## 9  9.399727e-05 0.7193775     4367383   4367463          81 ENSPREG00000000933
## 10 1.214571e-04 0.7193775     8864531   8864600          70 ENSPREG00000002350
## 11 1.267379e-04 0.7193775     8825906   8825952          47 ENSPREG00000023139
## 13 1.288502e-04 0.7193775    10806313  10806373          61 ENSPREG00000014890
## 14 1.320186e-04 0.7193775     9287677   9287703          27 ENSPREG00000001233
## 15 1.320186e-04 0.7193775     2578887   2578950          64 ENSPREG00000015120
## 16 1.320186e-04 0.7193775     2790037   2790092          56 ENSPREG00000001606
## 17 1.394117e-04 0.7193775    14118347  14118437          91 ENSPREG00000003007
## 18 1.679277e-04 0.7193775     2066128   2066167          40 ENSPREG00000009354
## 19 1.700400e-04 0.7193775     1269169   1269246          78 ENSPREG00000004582
## 20 1.721523e-04 0.7193775    10466014  10466030          17 ENSPREG00000020262
## 21 1.869384e-04 0.7193775     6174658   6174697          40 ENSPREG00000008175
## 22 1.996122e-04 0.7193775    12131403  12131455          53 ENSPREG00000012960
## 23 2.101737e-04 0.7193775    14521160  14521265         106 ENSPREG00000021212
##      gene_biotype gene_name
## 1  protein_coding      <NA>
## 2  protein_coding     btr30
## 3  protein_coding      <NA>
## 5  protein_coding      <NA>
## 6  protein_coding    asb14a
## 8  protein_coding     NFKB1
## 9  protein_coding    capn12
## 10 protein_coding     QRFPR
## 11 protein_coding     eif3c
## 13 protein_coding      <NA>
## 14 protein_coding      bbs1
## 15 protein_coding     kcnk9
## 16 protein_coding      <NA>
## 17 protein_coding      <NA>
## 18 protein_coding      dlg3
## 19 protein_coding      <NA>
## 20 protein_coding     cry3a
## 21 protein_coding      GNG4
## 22 protein_coding    efna2a
## 23 protein_coding      DAB1
rm(CvGgenes)
rm(CvGgenesdf)
ol2 <- findOverlaps(dmrseqCvL,my_genes)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215351.1, KK215360.1, KK215378.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215412.1, KK215414.1, KK215415.1, KK215418.1, KK215420.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215441.1, KK215443.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215454.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215472.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215501.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215512.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215526.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215546.1, KK215547.1, KK215553.1, KK215554.1, KK215556.1, KK215558.1, KK215559.1, KK215560.1, KK215561.1, KK215562.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215581.1, KK215582.1, KK215583.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215602.1, KK215603.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215627.1, KK215628.1, KK215629.1, KK215630.1, KK215632.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215639.1, KK215641.1, KK215642.1, KK215646.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215665.1, KK215668.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215683.1, KK215688.1, KK215692.1, KK215700.1, KK215701.1, KK215703.1, KK215704.1, KK215705.1, KK215706.1, KK215707.1, KK215709.1, KK215710.1, KK215711.1, KK215712.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215723.1, KK215724.1, KK215726.1, KK215727.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215741.1, KK215742.1, KK215748.1, KK215750.1, KK215752.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215758.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215780.1, KK215782.1, KK215783.1, KK215785.1, KK215788.1, KK215789.1, KK215792.1, KK215794.1, KK215795.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215816.1, KK215819.1, KK215825.1, KK215827.1, KK215832.1, KK215834.1, KK215838.1, KK215839.1, KK215840.1, KK215841.1, KK215842.1, KK215843.1, KK215849.1, KK215857.1, KK215860.1, KK215861.1, KK215863.1, KK215864.1, KK215870.1, KK215875.1, KK215878.1, KK215881.1, KK215885.1, KK215886.1, KK215891.1, KK215894.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215903.1, KK215907.1, KK215908.1, KK215909.1, KK215911.1, KK215915.1, KK215917.1, KK215918.1, KK215920.1, KK215921.1, KK215923.1, KK215927.1, KK215928.1, KK215929.1, KK215934.1, KK215935.1, KK215937.1, KK215938.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215949.1, KK215951.1, KK215952.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215962.1, KK215965.1, KK215969.1, KK215970.1, KK215971.1, KK215972.1, KK215973.1, KK215974.1, KK215976.1, KK215978.1, KK215979.1, KK215983.1, KK215989.1, KK215990.1, KK215993.1, KK215995.1, KK215997.1, KK215999.1, KK216000.1, KK216001.1, KK216006.1, KK216008.1, KK216012.1, KK216015.1, KK216017.1, KK216021.1, KK216023.1, KK216026.1, KK216027.1, KK216030.1, KK216032.1, KK216036.1, KK216037.1, KK216038.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216048.1, KK216049.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216064.1, KK216065.1, KK216068.1, KK216069.1, KK216071.1, KK216072.1, KK216074.1, KK216075.1, KK216076.1, KK216079.1, KK216080.1, KK216082.1, KK216083.1, KK216084.1, KK216087.1, KK216094.1, KK216096.1, KK216097.1, KK216103.1, KK216106.1, KK216109.1, KK216110.1, KK216111.1, KK216112.1, KK216114.1, KK216115.1, KK216118.1, KK216128.1, KK216131.1, KK216135.1, KK216140.1, KK216141.1, KK216143.1, KK216146.1, KK216150.1, KK216159.1, KK216162.1, KK216164.1, KK216165.1, KK216166.1, KK216168.1, KK216171.1, KK216174.1, KK216175.1, KK216176.1, KK216177.1, KK216181.1, KK216184.1, KK216190.1, KK216192.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216200.1, KK216202.1, KK216203.1, KK216206.1, KK216208.1, KK216212.1, KK216213.1, KK216214.1, KK216215.1, KK216219.1, KK216225.1, KK216226.1, KK216227.1, KK216229.1, KK216231.1, KK216232.1, KK216234.1, KK216235.1, KK216237.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216258.1, KK216259.1, KK216263.1, KK216264.1, KK216265.1, KK216266.1, KK216267.1, KK216272.1, KK216273.1, KK216275.1, KK216278.1, KK216280.1, KK216285.1, KK216287.1, KK216288.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216295.1, KK216304.1, KK216308.1, KK216310.1, KK216316.1, KK216317.1, KK216319.1, KK216320.1, KK216322.1, KK216323.1, KK216324.1, KK216325.1, KK216329.1, KK216341.1, KK216342.1, KK216345.1, KK216347.1, KK216351.1, KK216359.1, KK216364.1, KK216366.1, KK216369.1, KK216370.1, KK216379.1, KK216384.1, KK216385.1, KK216386.1, KK216387.1, KK216388.1, KK216389.1, KK216391.1, KK216392.1, KK216393.1, KK216394.1, KK216396.1, KK216402.1, KK216403.1, KK216404.1, KK216405.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216430.1, KK216431.1, KK216433.1, KK216436.1, KK216437.1, KK216438.1, KK216440.1, KK216443.1, KK216447.1, KK216452.1, KK216456.1, KK216457.1, KK216462.1, KK216467.1, KK216477.1, KK216486.1, KK216491.1, KK216492.1, KK216499.1, KK216503.1, KK216504.1, KK216506.1, KK216507.1, KK216511.1, KK216512.1, KK216520.1, KK216523.1, KK216530.1, KK216534.1, KK216538.1, KK216540.1, KK216556.1, KK216558.1, KK216570.1, KK216571.1, KK216572.1, KK216574.1, KK216586.1, KK216592.1, KK216595.1, KK216598.1, KK216604.1, KK216606.1, KK216609.1, KK216611.1, KK216615.1, KK216618.1, KK216622.1, KK216627.1, KK216630.1, KK216638.1, KK216641.1, KK216645.1, KK216646.1, KK216647.1, KK216648.1, KK216649.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216674.1, KK216685.1, KK216688.1, KK216696.1, KK216697.1, KK216704.1, KK216705.1, KK216707.1, KK216709.1, KK216710.1, KK216716.1, KK216717.1, KK216721.1, KK216723.1, KK216725.1, KK216726.1, KK216733.1, KK216737.1, KK216740.1, KK216746.1, KK216747.1, KK216748.1, KK216752.1, KK216761.1, KK216763.1, KK216764.1, KK216767.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216796.1, KK216803.1, KK216807.1, KK216815.1, KK216817.1, KK216820.1, KK216830.1, KK216841.1, KK216842.1, KK216846.1, KK216847.1, KK216851.1, KK216852.1, KK216865.1, KK216867.1, KK216868.1, KK216870.1, KK216871.1, KK216879.1, KK216880.1, KK216884.1, KK216887.1, KK216895.1, KK216902.1, KK216905.1, KK216908.1, KK216912.1, KK216914.1, KK216918.1, KK216921.1, KK216922.1, KK216930.1, KK216931.1, KK216932.1, KK216945.1, KK216953.1, KK216957.1, KK216968.1, KK216969.1, KK216970.1, KK216971.1, KK216974.1, KK216978.1, KK216980.1, KK216989.1, KK216990.1, KK216994.1, KK216995.1, KK217000.1, KK217002.1, KK217007.1, KK217008.1, KK217012.1, KK217014.1, KK217016.1, KK217019.1, KK217023.1, KK217024.1, KK217026.1, KK217040.1, KK217049.1, KK217053.1, KK217059.1, KK217063.1, KK217064.1, KK217065.1, KK217066.1, KK217068.1, KK217073.1, KK217076.1, KK217079.1, KK217082.1, KK217083.1, KK217088.1, KK217093.1, KK217095.1, KK217098.1, KK217100.1, KK217103.1, KK217104.1, KK217105.1, KK217111.1, KK217112.1, KK217114.1, KK217120.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217132.1, KK217133.1, KK217135.1, KK217137.1, KK217139.1, KK217140.1, KK217149.1, KK217150.1, KK217154.1, KK217160.1, KK217169.1, KK217172.
ol2
## Hits object with 56357 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         1       14834
##       [2]         3       22340
##       [3]         4        6146
##       [4]         5       21997
##       [5]         5       21998
##       ...       ...         ...
##   [56353]    111423        3088
##   [56354]    111429       11988
##   [56355]    111430        7310
##   [56356]    111436       20203
##   [56357]    111437       14928
##   -------
##   queryLength: 111437 / subjectLength: 23254
CvLgenes <- dmrseqCvL[queryHits(ol2)]
mygenesol2 <- my_genes[subjectHits(ol2)]
head(mygenesol2)
## GRanges object with 6 ranges and 3 metadata columns:
##         seqnames            ranges strand |            gene_id   gene_biotype
##            <Rle>         <IRanges>  <Rle> |        <character>    <character>
##   [1]       LG19 10324269-10333389      + | ENSPREG00000002350 protein_coding
##   [2] KK215293.1     156791-231222      - | ENSPREG00000013418 protein_coding
##   [3]       LG13 22005868-22053375      - | ENSPREG00000006590 protein_coding
##   [4] KK215283.1   1372895-1376892      - | ENSPREG00000019483 protein_coding
##   [5] KK215283.1   1376883-1386241      + | ENSPREG00000019522 protein_coding
##   [6]        LG8 18973748-18997964      + | ENSPREG00000011882 protein_coding
##         gene_name
##       <character>
##   [1]       QRFPR
##   [2]        <NA>
##   [3]    ankrd13b
##   [4]        sco2
##   [5]       calua
##   [6]    rapgefl1
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
CvLgenesdf <- as.data.frame(CvLgenes,row.names = 1:nrow(as.data.frame(ranges(CvLgenes))))
head(CvLgenesdf)
##     seqnames    start      end width strand   L      area       beta      stat
## 1       LG19 10333007 10333692   686      *  71 16.559670  0.5767663  18.99209
## 2 KK215293.1   186354   186845   492      *  61  5.160722  0.3911403  12.16515
## 3       LG13 22015858 22016352   495      *  82 14.226193  0.4397952  11.57442
## 4 KK215283.1  1376211  1376895   685      * 104 13.723096  0.3613973  11.54604
## 5 KK215283.1  1376211  1376895   685      * 104 13.723096  0.3613973  11.54604
## 6        LG8 18982718 18983377   660      *  60  7.212046 -0.3746378 -11.38354
##           pval      qval index.start index.end index.width
## 1 9.999990e-07 0.1114369     8673138   8673208          71
## 2 3.999996e-05 0.9103295      296821    296881          61
## 3 6.599993e-05 0.9103295     4374338   4374419          82
## 4 6.599993e-05 0.9103295       56943     57046         104
## 5 6.599993e-05 0.9103295       56943     57046         104
## 6 7.399993e-05 0.9103295    17405986  17406045          60
mygenesoldf2 <- as.data.frame(mygenesol2,row.names = 1:nrow(as.data.frame(ranges(mygenesol2))))
head(mygenesoldf2)
##     seqnames    start      end width strand            gene_id   gene_biotype
## 1       LG19 10324269 10333389  9121      + ENSPREG00000002350 protein_coding
## 2 KK215293.1   156791   231222 74432      - ENSPREG00000013418 protein_coding
## 3       LG13 22005868 22053375 47508      - ENSPREG00000006590 protein_coding
## 4 KK215283.1  1372895  1376892  3998      - ENSPREG00000019483 protein_coding
## 5 KK215283.1  1376883  1386241  9359      + ENSPREG00000019522 protein_coding
## 6        LG8 18973748 18997964 24217      + ENSPREG00000011882 protein_coding
##   gene_name
## 1     QRFPR
## 2      <NA>
## 3  ankrd13b
## 4      sco2
## 5     calua
## 6  rapgefl1
CvLgenesdf <- cbind(CvLgenesdf,mygenesoldf2[c("gene_id","gene_biotype","gene_name")])
CvLgenesdf$seqnames <- as.character(CvLgenesdf$seqnames)
CvLgeneschrdf <- CvLgenesdf[grep("LG",CvLgenesdf$seqnames),]
head(CvLgeneschrdf)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 3      LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6       LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 7      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
## 8      LG14  4297874  4299069  1196      * 45  9.873079 -0.4990115 -10.64895
## 10     LG12 21371716 21372025   310      * 58  3.735525 -0.3274811 -10.48784
##            pval      qval index.start index.end index.width            gene_id
## 1  9.999990e-07 0.1114369     8673138   8673208          71 ENSPREG00000002350
## 3  6.599993e-05 0.9103295     4374338   4374419          82 ENSPREG00000006590
## 6  7.399993e-05 0.9103295    17405986  17406045          60 ENSPREG00000011882
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  1.209999e-04 0.9103295     4766186   4766230          45 ENSPREG00000009813
## 10 1.389999e-04 0.9103295     3729020   3729077          58 ENSPREG00000019970
##      gene_biotype gene_name
## 1  protein_coding     QRFPR
## 3  protein_coding  ankrd13b
## 6  protein_coding  rapgefl1
## 7  protein_coding      <NA>
## 8  protein_coding    rab34b
## 10 protein_coding      <NA>
rm(CvLgenes)
rm(CvLgenesdf)
ol3 <- findOverlaps(dmrseqGvL,my_genes)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215341.1, KK215360.1, KK215378.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215402.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215412.1, KK215415.1, KK215418.1, KK215420.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215440.1, KK215441.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215546.1, KK215548.1, KK215549.1, KK215551.1, KK215553.1, KK215554.1, KK215559.1, KK215560.1, KK215561.1, KK215562.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215579.1, KK215581.1, KK215582.1, KK215583.1, KK215584.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215589.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215602.1, KK215603.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215620.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215628.1, KK215629.1, KK215630.1, KK215632.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215639.1, KK215641.1, KK215642.1, KK215644.1, KK215645.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215664.1, KK215668.1, KK215669.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215678.1, KK215684.1, KK215688.1, KK215692.1, KK215695.1, KK215699.1, KK215700.1, KK215701.1, KK215703.1, KK215705.1, KK215706.1, KK215707.1, KK215709.1, KK215711.1, KK215712.1, KK215715.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215724.1, KK215726.1, KK215727.1, KK215728.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215743.1, KK215745.1, KK215748.1, KK215750.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215771.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215782.1, KK215783.1, KK215786.1, KK215788.1, KK215789.1, KK215792.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215816.1, KK215818.1, KK215821.1, KK215825.1, KK215834.1, KK215836.1, KK215839.1, KK215842.1, KK215843.1, KK215847.1, KK215849.1, KK215852.1, KK215857.1, KK215858.1, KK215859.1, KK215860.1, KK215864.1, KK215867.1, KK215870.1, KK215872.1, KK215873.1, KK215877.1, KK215881.1, KK215885.1, KK215886.1, KK215890.1, KK215891.1, KK215893.1, KK215894.1, KK215897.1, KK215902.1, KK215905.1, KK215907.1, KK215908.1, KK215909.1, KK215910.1, KK215911.1, KK215914.1, KK215915.1, KK215917.1, KK215918.1, KK215920.1, KK215921.1, KK215927.1, KK215928.1, KK215929.1, KK215934.1, KK215938.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215946.1, KK215949.1, KK215951.1, KK215952.1, KK215960.1, KK215965.1, KK215967.1, KK215969.1, KK215970.1, KK215972.1, KK215974.1, KK215975.1, KK215976.1, KK215977.1, KK215978.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215993.1, KK215995.1, KK215997.1, KK215999.1, KK216000.1, KK216012.1, KK216017.1, KK216021.1, KK216023.1, KK216029.1, KK216030.1, KK216033.1, KK216034.1, KK216035.1, KK216038.1, KK216039.1, KK216041.1, KK216044.1, KK216048.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216063.1, KK216064.1, KK216067.1, KK216069.1, KK216072.1, KK216075.1, KK216076.1, KK216077.1, KK216079.1, KK216085.1, KK216086.1, KK216087.1, KK216089.1, KK216093.1, KK216094.1, KK216095.1, KK216099.1, KK216106.1, KK216109.1, KK216110.1, KK216114.1, KK216115.1, KK216120.1, KK216124.1, KK216128.1, KK216131.1, KK216134.1, KK216135.1, KK216140.1, KK216141.1, KK216142.1, KK216143.1, KK216150.1, KK216152.1, KK216157.1, KK216158.1, KK216162.1, KK216163.1, KK216165.1, KK216168.1, KK216169.1, KK216171.1, KK216174.1, KK216176.1, KK216177.1, KK216181.1, KK216184.1, KK216190.1, KK216192.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216201.1, KK216202.1, KK216203.1, KK216205.1, KK216212.1, KK216213.1, KK216214.1, KK216215.1, KK216217.1, KK216218.1, KK216219.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216231.1, KK216234.1, KK216235.1, KK216236.1, KK216240.1, KK216241.1, KK216242.1, KK216245.1, KK216248.1, KK216253.1, KK216256.1, KK216258.1, KK216259.1, KK216261.1, KK216264.1, KK216265.1, KK216266.1, KK216267.1, KK216269.1, KK216273.1, KK216278.1, KK216282.1, KK216284.1, KK216285.1, KK216287.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216293.1, KK216295.1, KK216303.1, KK216304.1, KK216306.1, KK216307.1, KK216310.1, KK216313.1, KK216315.1, KK216316.1, KK216317.1, KK216318.1, KK216319.1, KK216320.1, KK216323.1, KK216324.1, KK216325.1, KK216326.1, KK216329.1, KK216330.1, KK216331.1, KK216333.1, KK216336.1, KK216341.1, KK216342.1, KK216345.1, KK216351.1, KK216361.1, KK216363.1, KK216368.1, KK216369.1, KK216370.1, KK216374.1, KK216377.1, KK216383.1, KK216387.1, KK216388.1, KK216390.1, KK216391.1, KK216393.1, KK216394.1, KK216396.1, KK216400.1, KK216402.1, KK216403.1, KK216404.1, KK216410.1, KK216418.1, KK216420.1, KK216423.1, KK216427.1, KK216429.1, KK216430.1, KK216431.1, KK216437.1, KK216440.1, KK216442.1, KK216443.1, KK216447.1, KK216454.1, KK216456.1, KK216458.1, KK216462.1, KK216465.1, KK216467.1, KK216476.1, KK216478.1, KK216485.1, KK216486.1, KK216491.1, KK216492.1, KK216499.1, KK216500.1, KK216502.1, KK216506.1, KK216507.1, KK216508.1, KK216510.1, KK216511.1, KK216513.1, KK216515.1, KK216523.1, KK216526.1, KK216527.1, KK216530.1, KK216531.1, KK216534.1, KK216543.1, KK216552.1, KK216559.1, KK216566.1, KK216571.1, KK216574.1, KK216584.1, KK216596.1, KK216598.1, KK216602.1, KK216603.1, KK216606.1, KK216629.1, KK216630.1, KK216636.1, KK216638.1, KK216640.1, KK216643.1, KK216644.1, KK216648.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216665.1, KK216668.1, KK216671.1, KK216674.1, KK216678.1, KK216679.1, KK216686.1, KK216688.1, KK216696.1, KK216697.1, KK216702.1, KK216717.1, KK216725.1, KK216728.1, KK216731.1, KK216732.1, KK216733.1, KK216745.1, KK216748.1, KK216767.1, KK216771.1, KK216774.1, KK216775.1, KK216782.1, KK216784.1, KK216795.1, KK216796.1, KK216804.1, KK216807.1, KK216811.1, KK216813.1, KK216814.1, KK216817.1, KK216823.1, KK216841.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216866.1, KK216867.1, KK216870.1, KK216881.1, KK216882.1, KK216884.1, KK216892.1, KK216895.1, KK216896.1, KK216907.1, KK216908.1, KK216911.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216929.1, KK216934.1, KK216935.1, KK216936.1, KK216942.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216964.1, KK216965.1, KK216969.1, KK216971.1, KK216973.1, KK216977.1, KK216978.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216995.1, KK216998.1, KK216999.1, KK217001.1, KK217003.1, KK217007.1, KK217008.1, KK217010.1, KK217011.1, KK217012.1, KK217016.1, KK217017.1, KK217019.1, KK217021.1, KK217032.1, KK217040.1, KK217049.1, KK217059.1, KK217063.1, KK217076.1, KK217077.1, KK217080.1, KK217083.1, KK217090.1, KK217091.1, KK217098.1, KK217100.1, KK217101.1, KK217104.1, KK217105.1, KK217111.1, KK217120.1, KK217123.1, KK217128.1, KK217133.1, KK217135.1, KK217147.1, KK217151.1, KK217161.1, KK217163.1, KK217174.1, KK217179.1, KK217182.1, KK217183.1, KK217186.1, KK217187.1, KK217189.1, KK217190.1, KK217193.1, KK217200.1, KK217203.1, KK217204.1, KK217206.1, KK217209.1, KK217228.1, KK217233.1, KK217237.1, KK217238.1, KK217241.1, KK217242.
ol3
## Hits object with 45925 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         1       14440
##       [2]         2       21997
##       [3]         2       21998
##       [4]         5         891
##       [5]         6        6028
##       ...       ...         ...
##   [45921]     91515       14451
##   [45922]     91516        4865
##   [45923]     91519        1058
##   [45924]     91520        5503
##   [45925]     91522       16070
##   -------
##   queryLength: 91524 / subjectLength: 23254
GvLgenes <- dmrseqGvL[queryHits(ol3)]
mygenesol3 <- my_genes[subjectHits(ol3)]
head(mygenesol3)
## GRanges object with 6 ranges and 3 metadata columns:
##         seqnames            ranges strand |            gene_id   gene_biotype
##            <Rle>         <IRanges>  <Rle> |        <character>    <character>
##   [1]       LG11 28457673-28466140      + | ENSPREG00000010167 protein_coding
##   [2] KK215283.1   1372895-1376892      - | ENSPREG00000019483 protein_coding
##   [3] KK215283.1   1376883-1386241      + | ENSPREG00000019522 protein_coding
##   [4]        LG2 28489230-28494380      + | ENSPREG00000001027 protein_coding
##   [5]       LG13 18160798-18170662      - | ENSPREG00000001265 protein_coding
##   [6] KK215287.1     939495-948585      - | ENSPREG00000007395 protein_coding
##         gene_name
##       <character>
##   [1]        ncdn
##   [2]        sco2
##   [3]       calua
##   [4]       casq2
##   [5]        <NA>
##   [6]       wdr74
##   -------
##   seqinfo: 463 sequences from an unspecified genome; no seqlengths
GvLgenesdf <- as.data.frame(GvLgenes,row.names = 1:nrow(as.data.frame(ranges(GvLgenes))))
head(GvLgenesdf)
##     seqnames    start      end width strand   L      area       beta      stat
## 1       LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 2 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 3 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 4        LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 5       LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 6 KK215287.1   944627   944828   202      *  36  4.299457 -0.4584372 -12.68316
##           pval      qval index.start index.end index.width
## 1 7.144039e-06 0.6538511     3678849   3678956         108
## 2 1.786010e-05 0.7492043       65611     65766         156
## 3 1.786010e-05 0.7492043       65611     65766         156
## 4 5.477097e-05 0.7492043    11413014  11413078          65
## 5 5.596164e-05 0.7492043     4929871   4929965          95
## 6 6.072433e-05 0.7492043      223719    223754          36
mygenesoldf3 <- as.data.frame(mygenesol3,row.names = 1:nrow(as.data.frame(ranges(mygenesol3))))
head(mygenesoldf3)
##     seqnames    start      end width strand            gene_id   gene_biotype
## 1       LG11 28457673 28466140  8468      + ENSPREG00000010167 protein_coding
## 2 KK215283.1  1372895  1376892  3998      - ENSPREG00000019483 protein_coding
## 3 KK215283.1  1376883  1386241  9359      + ENSPREG00000019522 protein_coding
## 4        LG2 28489230 28494380  5151      + ENSPREG00000001027 protein_coding
## 5       LG13 18160798 18170662  9865      - ENSPREG00000001265 protein_coding
## 6 KK215287.1   939495   948585  9091      - ENSPREG00000007395 protein_coding
##   gene_name
## 1      ncdn
## 2      sco2
## 3     calua
## 4     casq2
## 5      <NA>
## 6     wdr74
GvLgenesdf <- cbind(GvLgenesdf,mygenesoldf3[c("gene_id","gene_biotype","gene_name")])
GvLgenesdf$seqnames <- as.character(GvLgenesdf$seqnames)
GvLgeneschrdf <- GvLgenesdf[grep("LG",GvLgenesdf$seqnames),]
head(GvLgeneschrdf)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 4       LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 5      LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7      LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10      LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##            pval      qval index.start index.end index.width            gene_id
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010167
## 4  5.477097e-05 0.7492043    11413014  11413078          65 ENSPREG00000001027
## 5  5.596164e-05 0.7492043     4929871   4929965          95 ENSPREG00000001265
## 7  6.548703e-05 0.7492043     3123427   3123501          75 ENSPREG00000021580
## 9  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022808
## 10 9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
##      gene_biotype gene_name
## 1  protein_coding      ncdn
## 4  protein_coding     casq2
## 5  protein_coding      <NA>
## 7  protein_coding    jazf1a
## 9  protein_coding      <NA>
## 10 protein_coding    asb14a
rm(GvLgenes)
rm(GvLgenesdf)

dmrs annotated to CpG islands

ol1 <- findOverlaps(dmrseqCvG,my_CpGislands)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215310.1, KK215370.1, KK215371.1, KK215372.1, KK215373.1, KK215378.1, KK215380.1, KK215381.1, KK215393.1, KK215396.1, KK215405.1, KK215406.1, KK215417.1, KK215421.1, KK215422.1, KK215430.1, KK215433.1, KK215435.1, KK215437.1, KK215438.1, KK215440.1, KK215442.1, KK215454.1, KK215456.1, KK215458.1, KK215461.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215468.1, KK215472.1, KK215474.1, KK215480.1, KK215482.1, KK215483.1, KK215484.1, KK215485.1, KK215486.1, KK215487.1, KK215494.1, KK215497.1, KK215498.1, KK215501.1, KK215503.1, KK215504.1, KK215506.1, KK215508.1, KK215515.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215531.1, KK215533.1, KK215536.1, KK215538.1, KK215541.1, KK215544.1, KK215545.1, KK215547.1, KK215548.1, KK215549.1, KK215551.1, KK215556.1, KK215559.1, KK215560.1, KK215565.1, KK215570.1, KK215572.1, KK215573.1, KK215574.1, KK215577.1, KK215580.1, KK215585.1, KK215591.1, KK215592.1, KK215593.1, KK215595.1, KK215598.1, KK215609.1, KK215614.1, KK215615.1, KK215620.1, KK215621.1, KK215623.1, KK215625.1, KK215626.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215642.1, KK215643.1, KK215645.1, KK215647.1, KK215649.1, KK215651.1, KK215652.1, KK215654.1, KK215656.1, KK215657.1, KK215661.1, KK215662.1, KK215663.1, KK215665.1, KK215668.1, KK215671.1, KK215673.1, KK215675.1, KK215677.1, KK215681.1, KK215684.1, KK215687.1, KK215688.1, KK215691.1, KK215692.1, KK215695.1, KK215697.1, KK215698.1, KK215703.1, KK215705.1, KK215708.1, KK215710.1, KK215717.1, KK215720.1, KK215721.1, KK215724.1, KK215727.1, KK215728.1, KK215730.1, KK215734.1, KK215735.1, KK215736.1, KK215738.1, KK215741.1, KK215742.1, KK215743.1, KK215756.1, KK215757.1, KK215760.1, KK215761.1, KK215762.1, KK215763.1, KK215767.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215779.1, KK215780.1, KK215785.1, KK215786.1, KK215787.1, KK215789.1, KK215790.1, KK215794.1, KK215795.1, KK215798.1, KK215800.1, KK215802.1, KK215803.1, KK215804.1, KK215808.1, KK215809.1, KK215810.1, KK215813.1, KK215814.1, KK215815.1, KK215816.1, KK215824.1, KK215825.1, KK215827.1, KK215828.1, KK215834.1, KK215838.1, KK215843.1, KK215844.1, KK215849.1, KK215854.1, KK215856.1, KK215857.1, KK215858.1, KK215859.1, KK215861.1, KK215863.1, KK215864.1, KK215873.1, KK215875.1, KK215878.1, KK215880.1, KK215881.1, KK215885.1, KK215886.1, KK215887.1, KK215888.1, KK215890.1, KK215891.1, KK215895.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215909.1, KK215911.1, KK215914.1, KK215915.1, KK215918.1, KK215921.1, KK215923.1, KK215928.1, KK215934.1, KK215942.1, KK215943.1, KK215945.1, KK215947.1, KK215949.1, KK215951.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215968.1, KK215969.1, KK215970.1, KK215973.1, KK215976.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215993.1, KK215994.1, KK215997.1, KK216000.1, KK216001.1, KK216012.1, KK216014.1, KK216015.1, KK216017.1, KK216018.1, KK216025.1, KK216026.1, KK216028.1, KK216029.1, KK216030.1, KK216032.1, KK216033.1, KK216034.1, KK216035.1, KK216037.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216049.1, KK216053.1, KK216063.1, KK216064.1, KK216065.1, KK216066.1, KK216068.1, KK216069.1, KK216072.1, KK216075.1, KK216076.1, KK216079.1, KK216082.1, KK216084.1, KK216085.1, KK216086.1, KK216089.1, KK216093.1, KK216097.1, KK216100.1, KK216107.1, KK216114.1, KK216116.1, KK216120.1, KK216122.1, KK216124.1, KK216128.1, KK216130.1, KK216133.1, KK216134.1, KK216135.1, KK216136.1, KK216141.1, KK216142.1, KK216143.1, KK216147.1, KK216152.1, KK216155.1, KK216157.1, KK216158.1, KK216165.1, KK216166.1, KK216169.1, KK216171.1, KK216174.1, KK216184.1, KK216186.1, KK216190.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216200.1, KK216208.1, KK216212.1, KK216215.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216228.1, KK216230.1, KK216232.1, KK216237.1, KK216238.1, KK216240.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216259.1, KK216260.1, KK216261.1, KK216264.1, KK216266.1, KK216270.1, KK216278.1, KK216280.1, KK216281.1, KK216284.1, KK216287.1, KK216289.1, KK216290.1, KK216294.1, KK216295.1, KK216306.1, KK216310.1, KK216313.1, KK216320.1, KK216322.1, KK216324.1, KK216325.1, KK216329.1, KK216330.1, KK216336.1, KK216341.1, KK216342.1, KK216351.1, KK216352.1, KK216355.1, KK216359.1, KK216360.1, KK216363.1, KK216366.1, KK216370.1, KK216371.1, KK216377.1, KK216380.1, KK216383.1, KK216384.1, KK216389.1, KK216391.1, KK216394.1, KK216396.1, KK216402.1, KK216404.1, KK216405.1, KK216408.1, KK216410.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216423.1, KK216425.1, KK216428.1, KK216432.1, KK216433.1, KK216438.1, KK216440.1, KK216442.1, KK216445.1, KK216451.1, KK216452.1, KK216453.1, KK216456.1, KK216457.1, KK216458.1, KK216459.1, KK216462.1, KK216468.1, KK216477.1, KK216479.1, KK216482.1, KK216492.1, KK216502.1, KK216504.1, KK216506.1, KK216508.1, KK216510.1, KK216511.1, KK216512.1, KK216513.1, KK216514.1, KK216515.1, KK216523.1, KK216526.1, KK216530.1, KK216531.1, KK216538.1, KK216548.1, KK216552.1, KK216553.1, KK216556.1, KK216569.1, KK216571.1, KK216572.1, KK216574.1, KK216576.1, KK216592.1, KK216599.1, KK216606.1, KK216607.1, KK216610.1, KK216615.1, KK216619.1, KK216640.1, KK216647.1, KK216651.1, KK216657.1, KK216661.1, KK216665.1, KK216672.1, KK216674.1, KK216678.1, KK216680.1, KK216685.1, KK216691.1, KK216699.1, KK216709.1, KK216712.1, KK216714.1, KK216716.1, KK216717.1, KK216725.1, KK216726.1, KK216732.1, KK216737.1, KK216740.1, KK216745.1, KK216746.1, KK216748.1, KK216752.1, KK216758.1, KK216763.1, KK216773.1, KK216779.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216800.1, KK216814.1, KK216815.1, KK216817.1, KK216824.1, KK216830.1, KK216831.1, KK216834.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216863.1, KK216865.1, KK216867.1, KK216870.1, KK216873.1, KK216879.1, KK216887.1, KK216896.1, KK216898.1, KK216899.1, KK216903.1, KK216905.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216922.1, KK216923.1, KK216930.1, KK216931.1, KK216933.1, KK216934.1, KK216938.1, KK216942.1, KK216943.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216963.1, KK216964.1, KK216965.1, KK216968.1, KK216971.1, KK216973.1, KK216974.1, KK216975.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216999.1, KK217000.1, KK217001.1, KK217002.1, KK217003.1, KK217007.1, KK217012.1, KK217019.1, KK217028.1, KK217032.1, KK217037.1, KK217059.1, KK217060.1, KK217063.1, KK217065.1, KK217066.1, KK217072.1, KK217074.1, KK217076.1, KK217077.1, KK217079.1, KK217082.1, KK217083.1, KK217086.1, KK217088.1, KK217093.1, KK217098.1, KK217101.1, KK217103.1, KK217105.1, KK217112.1, KK217114.1, KK217119.1, KK217120.1, KK217121.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217135.1, KK217140.1, KK217146.1, KK217147.1, KK217182.1, KK217185.1, KK217193.1, KK217195.1, KK217196.1, KK217203.1, KK217204.1, KK217206.1, KK217207.1, KK217214.1, KK217222.1, KK217227.1, KK217228.1, KK217233.1, KK217237.1, KK217240.1, KK217242.1, KK217244.1, KK217249.1, KK217255.1, KK217257.1, KK217263.1, KK217265.1, KK217279.1, KK217284.1, KK217289.1, KK217295.1, KK217303.1, KK217305.1, KK217313.1, KK217314.1, KK217320.1, KK217323.1, KK217324.1, KK217325.1, KK217331.1, KK217334.1, KK217343.1, KK217345.1, KK217346.1, KK217360.1, KK217363.1, KK217379.1, KK217382.1, KK217384.1, KK217385.1, KK217388.1, KK217389.1, KK217390.1, KK217396.1, KK217397.1, KK217398.1, KK217401.1, KK217402.1, KK217416.1, KK217423.1, KK217426.1, KK217431.1, KK217432.1, KK217437.1, KK217442.1, KK217445.1, KK217446.1, KK217449.1, KK217452.1, KK217461.1, KK217470.1, KK217471.1, KK217473.1, KK217475.1, KK217478.1, KK217479.1, KK217482.1, KK217484.1, KK217485.1, KK217486.1, KK217490.1, KK217499.1, KK217508.1, KK217510.1, KK217523.1, KK217528.1, KK217533.1, KK217537.1, KK217540.1, KK217548.1, KK217551.1, KK217554.1, KK217555.1, KK217558.1, KK217559.1, KK217567.1, KK217571.1, KK217572.1, KK217585.1, KK217586.1, KK217593.1, KK217596.1, KK217614.1, KK217616.1, KK217623.1, KK217630.1, KK217633.1, KK217635.
ol1
## Hits object with 6624 hits and 0 metadata columns:
##          queryHits subjectHits
##          <integer>   <integer>
##      [1]         2       32069
##      [2]         3       21175
##      [3]         4       57357
##      [4]         5       58973
##      [5]         6        4736
##      ...       ...         ...
##   [6620]    110673       26710
##   [6621]    110694       24046
##   [6622]    110697       30955
##   [6623]    110721       47416
##   [6624]    110773       43887
##   -------
##   queryLength: 110780 / subjectLength: 60897
CvGCpGislands <- dmrseqCvG[queryHits(ol1)]
my_CpGislandsol1 <- my_CpGislands[subjectHits(ol1)]
head(CvGCpGislands)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG13 18160946-18161700      * |        75  17.10434  0.480479
##   [2]        LG8 27368425-27368499      * |        22   1.10760 -0.359863
##   [3] KK215287.1     628700-629071      * |        42   2.46231 -0.357702
##   [4] KK215308.1       92510-92874      * |        65   4.00345 -0.303095
##   [5]        LG2 18092802-18093635      * |        53   9.37373 -0.397850
##   [6]        LG5   2971274-2971545      * |        61   8.49567  0.378574
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]   12.3558 4.01337e-05  0.719377   4371608-4371682
##   [2]  -12.3461 4.11898e-05  0.719377 18010981-18011002
##   [3]  -12.2466 4.22460e-05  0.719377     186337-186378
##   [4]  -12.1655 4.43583e-05  0.719377     437886-437950
##   [5]  -12.0724 4.54144e-05  0.719377   9863892-9863944
##   [6]   11.6533 6.44251e-05  0.719377 14903599-14903659
##   -------
##   seqinfo: 1181 sequences from an unspecified genome; no seqlengths
my_CpGislandsol1
## GRanges object with 6624 ranges and 2 metadata columns:
##            seqnames            ranges strand |   source             ID
##               <Rle>         <IRanges>  <Rle> | <factor>    <character>
##      [1]       LG13 18160935-18161432      + |  cpgplot      LG13.1141
##      [2]        LG8 27368282-27368834      + |  cpgplot       LG8.2475
##      [3] KK215287.1     628647-628865      + |  cpgplot KK215287.1.117
##      [4] KK215308.1       92486-92833      + |  cpgplot  KK215308.1.25
##      [5]        LG2 18092818-18093060      + |  cpgplot       LG2.1904
##      ...        ...               ...    ... .      ...            ...
##   [6620]       LG11   7839037-7839328      + |  cpgplot       LG11.575
##   [6621]       LG10   4122858-4123057      + |  cpgplot       LG10.312
##   [6622]       LG13     647418-647839      + |  cpgplot        LG13.27
##   [6623]       LG19 23592736-23592941      + |  cpgplot      LG19.2566
##   [6624]       LG18 12011108-12011511      + |  cpgplot      LG18.1052
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
CvGCpGislandsdf <- as.data.frame(CvGCpGislands,row.names = 1:nrow(as.data.frame(ranges(CvGCpGislands))))
str(CvGCpGislandsdf)
## 'data.frame':    6624 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1181 levels "KK215283.1","KK215284.1",..: 1163 1180 5 26 1170 1177 1 1160 1163 316 ...
##  $ start      : int  18160946 27368425 628700 92510 18092802 2971274 934758 32171882 18052556 8328 ...
##  $ end        : int  18161700 27368499 629071 92874 18093635 2971545 935340 32172301 18054100 9236 ...
##  $ width      : int  755 75 372 365 834 272 583 420 1545 909 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  75 22 42 65 53 61 78 46 81 45 ...
##  $ area       : num  17.1 1.11 2.46 4 9.37 ...
##  $ beta       : num  0.48 -0.36 -0.358 -0.303 -0.398 ...
##  $ stat       : num  12.4 -12.3 -12.2 -12.2 -12.1 ...
##  $ pval       : num  4.01e-05 4.12e-05 4.22e-05 4.44e-05 4.54e-05 ...
##  $ qval       : num  0.719 0.719 0.719 0.719 0.719 ...
##  $ index.start: int  4371608 18010981 186337 437886 9863892 14903599 37410 2481310 4367383 672143 ...
##  $ index.end  : int  4371682 18011002 186378 437950 9863944 14903659 37487 2481355 4367463 672187 ...
##  $ index.width: int  75 22 42 65 53 61 78 46 81 45 ...
my_CpGislandsol1 <- as.data.frame(my_CpGislandsol1,row.names = 1:nrow(as.data.frame(ranges(my_CpGislandsol1))))
head(my_CpGislandsol1)
##     seqnames    start      end width strand  source             ID
## 1       LG13 18160935 18161432   498      + cpgplot      LG13.1141
## 2        LG8 27368282 27368834   553      + cpgplot       LG8.2475
## 3 KK215287.1   628647   628865   219      + cpgplot KK215287.1.117
## 4 KK215308.1    92486    92833   348      + cpgplot  KK215308.1.25
## 5        LG2 18092818 18093060   243      + cpgplot       LG2.1904
## 6        LG5  2971248  2971572   325      + cpgplot        LG5.532
CvGCpGislandsdf <- cbind(CvGCpGislandsdf,my_CpGislandsol1[c("source","ID")])
CvGCpGislandsdf$seqnames <- as.character(CvGCpGislandsdf$seqnames)
head(CvGCpGislandsdf)
##     seqnames    start      end width strand  L      area       beta      stat
## 1       LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2        LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 3 KK215287.1   628700   629071   372      * 42  2.462310 -0.3577019 -12.24660
## 4 KK215308.1    92510    92874   365      * 65  4.003455 -0.3030945 -12.16552
## 5        LG2 18092802 18093635   834      * 53  9.373725 -0.3978501 -12.07243
## 6        LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
##           pval      qval index.start index.end index.width  source
## 1 4.013367e-05 0.7193775     4371608   4371682          75 cpgplot
## 2 4.118982e-05 0.7193775    18010981  18011002          22 cpgplot
## 3 4.224596e-05 0.7193775      186337    186378          42 cpgplot
## 4 4.435826e-05 0.7193775      437886    437950          65 cpgplot
## 5 4.541441e-05 0.7193775     9863892   9863944          53 cpgplot
## 6 6.442510e-05 0.7193775    14903599  14903659          61 cpgplot
##               ID
## 1      LG13.1141
## 2       LG8.2475
## 3 KK215287.1.117
## 4  KK215308.1.25
## 5       LG2.1904
## 6        LG5.532
CvGCpGislandschrdf <- CvGCpGislandsdf[grep("LG",CvGCpGislandsdf$seqnames),]
head(CvGCpGislandschrdf)
##   seqnames    start      end width strand  L      area       beta      stat
## 1     LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 5      LG2 18092802 18093635   834      * 53  9.373725 -0.3978501 -12.07243
## 6      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8     LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
## 9     LG13 18052556 18054100  1545      * 81 10.961955 -0.3413481 -11.11704
##           pval      qval index.start index.end index.width  source        ID
## 1 4.013367e-05 0.7193775     4371608   4371682          75 cpgplot LG13.1141
## 2 4.118982e-05 0.7193775    18010981  18011002          22 cpgplot  LG8.2475
## 5 4.541441e-05 0.7193775     9863892   9863944          53 cpgplot  LG2.1904
## 6 6.442510e-05 0.7193775    14903599  14903659          61 cpgplot   LG5.532
## 8 9.082882e-05 0.7193775     2481310   2481355          46 cpgplot LG10.2195
## 9 9.399727e-05 0.7193775     4367383   4367463          81 cpgplot LG13.1122
CvGCpGislandschrdf <- CvGCpGislandschrdf[order(CvGCpGislandschrdf[,11]), ]
head(CvGCpGislandschrdf,10)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2       LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 5       LG2 18092802 18093635   834      * 53  9.373725 -0.3978501 -12.07243
## 6       LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8      LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
## 9      LG13 18052556 18054100  1545      * 81 10.961955 -0.3413481 -11.11704
## 11     LG19 10333007 10333692   686      * 70 10.588759  0.4116465  10.86281
## 12     LG19  8889655  8889899   245      * 47  2.420966 -0.2756728 -10.81171
## 14     LG20 10526898 10527306   409      * 61  5.646018  0.2998656  10.73088
## 15     LG11 10641658 10642177   520      * 56  6.750824  0.4028755  10.69685
##            pval      qval index.start index.end index.width  source        ID
## 1  4.013367e-05 0.7193775     4371608   4371682          75 cpgplot LG13.1141
## 2  4.118982e-05 0.7193775    18010981  18011002          22 cpgplot  LG8.2475
## 5  4.541441e-05 0.7193775     9863892   9863944          53 cpgplot  LG2.1904
## 6  6.442510e-05 0.7193775    14903599  14903659          61 cpgplot   LG5.532
## 8  9.082882e-05 0.7193775     2481310   2481355          46 cpgplot LG10.2195
## 9  9.399727e-05 0.7193775     4367383   4367463          81 cpgplot LG13.1122
## 11 1.214571e-04 0.7193775     8864531   8864600          70 cpgplot LG19.1464
## 12 1.267379e-04 0.7193775     8825906   8825952          47 cpgplot LG19.1372
## 14 1.288502e-04 0.7193775    10806313  10806373          61 cpgplot  LG20.800
## 15 1.320186e-04 0.7193775     2790037   2790092          56 cpgplot  LG11.783
rm(CvGCpGislands)
rm(CvGCpGislandsdf)
ol1 <- findOverlaps(dmrseqCvL,my_CpGislands)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215310.1, KK215370.1, KK215371.1, KK215372.1, KK215373.1, KK215378.1, KK215381.1, KK215382.1, KK215393.1, KK215396.1, KK215404.1, KK215405.1, KK215406.1, KK215412.1, KK215414.1, KK215417.1, KK215420.1, KK215421.1, KK215422.1, KK215423.1, KK215430.1, KK215433.1, KK215435.1, KK215437.1, KK215438.1, KK215442.1, KK215454.1, KK215456.1, KK215458.1, KK215461.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215468.1, KK215472.1, KK215474.1, KK215480.1, KK215482.1, KK215483.1, KK215484.1, KK215485.1, KK215486.1, KK215487.1, KK215494.1, KK215497.1, KK215498.1, KK215501.1, KK215503.1, KK215504.1, KK215506.1, KK215508.1, KK215512.1, KK215515.1, KK215519.1, KK215521.1, KK215522.1, KK215523.1, KK215524.1, KK215525.1, KK215526.1, KK215528.1, KK215531.1, KK215533.1, KK215534.1, KK215536.1, KK215538.1, KK215541.1, KK215544.1, KK215545.1, KK215546.1, KK215547.1, KK215554.1, KK215556.1, KK215559.1, KK215560.1, KK215562.1, KK215565.1, KK215570.1, KK215573.1, KK215574.1, KK215577.1, KK215580.1, KK215582.1, KK215585.1, KK215591.1, KK215592.1, KK215593.1, KK215595.1, KK215598.1, KK215609.1, KK215612.1, KK215613.1, KK215615.1, KK215621.1, KK215625.1, KK215626.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215642.1, KK215643.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215656.1, KK215657.1, KK215661.1, KK215662.1, KK215663.1, KK215665.1, KK215668.1, KK215671.1, KK215673.1, KK215675.1, KK215677.1, KK215681.1, KK215688.1, KK215691.1, KK215692.1, KK215698.1, KK215703.1, KK215705.1, KK215707.1, KK215708.1, KK215710.1, KK215712.1, KK215717.1, KK215720.1, KK215721.1, KK215723.1, KK215724.1, KK215727.1, KK215730.1, KK215731.1, KK215734.1, KK215735.1, KK215736.1, KK215738.1, KK215741.1, KK215742.1, KK215748.1, KK215756.1, KK215757.1, KK215758.1, KK215761.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215780.1, KK215785.1, KK215787.1, KK215789.1, KK215790.1, KK215794.1, KK215795.1, KK215798.1, KK215800.1, KK215802.1, KK215803.1, KK215804.1, KK215808.1, KK215809.1, KK215810.1, KK215813.1, KK215814.1, KK215816.1, KK215819.1, KK215824.1, KK215825.1, KK215827.1, KK215828.1, KK215834.1, KK215838.1, KK215839.1, KK215840.1, KK215842.1, KK215843.1, KK215844.1, KK215849.1, KK215856.1, KK215857.1, KK215860.1, KK215861.1, KK215863.1, KK215864.1, KK215870.1, KK215871.1, KK215875.1, KK215878.1, KK215879.1, KK215881.1, KK215885.1, KK215886.1, KK215887.1, KK215888.1, KK215891.1, KK215895.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215903.1, KK215908.1, KK215909.1, KK215911.1, KK215915.1, KK215918.1, KK215920.1, KK215921.1, KK215923.1, KK215927.1, KK215928.1, KK215934.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215949.1, KK215950.1, KK215951.1, KK215952.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215969.1, KK215970.1, KK215971.1, KK215972.1, KK215973.1, KK215976.1, KK215978.1, KK215979.1, KK215983.1, KK215993.1, KK215997.1, KK216000.1, KK216001.1, KK216006.1, KK216012.1, KK216015.1, KK216017.1, KK216026.1, KK216030.1, KK216032.1, KK216037.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216048.1, KK216049.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216064.1, KK216065.1, KK216068.1, KK216069.1, KK216072.1, KK216075.1, KK216076.1, KK216079.1, KK216080.1, KK216082.1, KK216083.1, KK216084.1, KK216087.1, KK216092.1, KK216097.1, KK216101.1, KK216106.1, KK216107.1, KK216108.1, KK216110.1, KK216112.1, KK216114.1, KK216116.1, KK216128.1, KK216130.1, KK216131.1, KK216135.1, KK216136.1, KK216140.1, KK216141.1, KK216143.1, KK216146.1, KK216159.1, KK216161.1, KK216164.1, KK216165.1, KK216166.1, KK216168.1, KK216171.1, KK216174.1, KK216176.1, KK216181.1, KK216184.1, KK216190.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216200.1, KK216202.1, KK216206.1, KK216208.1, KK216212.1, KK216214.1, KK216215.1, KK216225.1, KK216226.1, KK216227.1, KK216228.1, KK216230.1, KK216231.1, KK216232.1, KK216234.1, KK216237.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216258.1, KK216259.1, KK216263.1, KK216264.1, KK216266.1, KK216267.1, KK216278.1, KK216280.1, KK216287.1, KK216288.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216295.1, KK216304.1, KK216310.1, KK216317.1, KK216319.1, KK216320.1, KK216322.1, KK216324.1, KK216325.1, KK216329.1, KK216332.1, KK216341.1, KK216342.1, KK216345.1, KK216347.1, KK216351.1, KK216355.1, KK216359.1, KK216366.1, KK216369.1, KK216370.1, KK216379.1, KK216380.1, KK216384.1, KK216385.1, KK216387.1, KK216388.1, KK216389.1, KK216391.1, KK216393.1, KK216394.1, KK216396.1, KK216402.1, KK216403.1, KK216404.1, KK216405.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216430.1, KK216431.1, KK216433.1, KK216437.1, KK216438.1, KK216440.1, KK216443.1, KK216452.1, KK216456.1, KK216457.1, KK216462.1, KK216467.1, KK216477.1, KK216479.1, KK216486.1, KK216491.1, KK216492.1, KK216503.1, KK216504.1, KK216506.1, KK216511.1, KK216512.1, KK216520.1, KK216523.1, KK216530.1, KK216534.1, KK216538.1, KK216556.1, KK216558.1, KK216570.1, KK216571.1, KK216572.1, KK216574.1, KK216586.1, KK216592.1, KK216595.1, KK216598.1, KK216604.1, KK216606.1, KK216609.1, KK216611.1, KK216615.1, KK216618.1, KK216622.1, KK216630.1, KK216641.1, KK216645.1, KK216646.1, KK216647.1, KK216649.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216674.1, KK216685.1, KK216688.1, KK216697.1, KK216699.1, KK216704.1, KK216705.1, KK216707.1, KK216709.1, KK216710.1, KK216716.1, KK216717.1, KK216721.1, KK216723.1, KK216725.1, KK216726.1, KK216733.1, KK216737.1, KK216739.1, KK216740.1, KK216741.1, KK216746.1, KK216747.1, KK216748.1, KK216752.1, KK216761.1, KK216763.1, KK216764.1, KK216767.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216796.1, KK216803.1, KK216807.1, KK216815.1, KK216817.1, KK216820.1, KK216830.1, KK216846.1, KK216847.1, KK216851.1, KK216852.1, KK216865.1, KK216867.1, KK216868.1, KK216870.1, KK216871.1, KK216879.1, KK216880.1, KK216884.1, KK216887.1, KK216891.1, KK216895.1, KK216902.1, KK216905.1, KK216908.1, KK216912.1, KK216914.1, KK216918.1, KK216921.1, KK216922.1, KK216930.1, KK216931.1, KK216932.1, KK216938.1, KK216945.1, KK216953.1, KK216957.1, KK216968.1, KK216969.1, KK216970.1, KK216971.1, KK216974.1, KK216978.1, KK216980.1, KK216989.1, KK216990.1, KK216994.1, KK216995.1, KK217000.1, KK217002.1, KK217007.1, KK217008.1, KK217012.1, KK217014.1, KK217016.1, KK217019.1, KK217023.1, KK217024.1, KK217026.1, KK217040.1, KK217049.1, KK217053.1, KK217059.1, KK217063.1, KK217064.1, KK217065.1, KK217066.1, KK217068.1, KK217073.1, KK217076.1, KK217079.1, KK217082.1, KK217083.1, KK217088.1, KK217093.1, KK217095.1, KK217098.1, KK217100.1, KK217103.1, KK217104.1, KK217105.1, KK217112.1, KK217114.1, KK217120.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217132.1, KK217133.1, KK217135.1, KK217137.1, KK217139.1, KK217140.1, KK217149.1, KK217150.1, KK217154.1, KK217160.1, KK217169.1, KK217172.1, KK217174.1, KK217176.1, KK217182.1, KK217186.1, KK217187.1, KK217191.1, KK217193.1, KK217195.1, KK217203.1, KK217204.1, KK217206.1, KK217210.1, KK217215.1, KK217216.1, KK217224.1, KK217228.1, KK217229.1, KK217233.1, KK217237.1, KK217254.1, KK217257.1, KK217263.1, KK217265.1, KK217266.1, KK217272.1, KK217280.1, KK217284.1, KK217291.1, KK217295.1, KK217303.1, KK217311.1, KK217314.1, KK217322.1, KK217323.1, KK217324.1, KK217325.1, KK217328.1, KK217330.1, KK217331.1, KK217342.1, KK217346.1, KK217352.1, KK217353.1, KK217354.1, KK217359.1, KK217360.1, KK217363.1, KK217369.1, KK217373.1, KK217379.1, KK217384.1, KK217388.1, KK217389.1, KK217396.1, KK217397.1, KK217399.1, KK217414.1, KK217416.1, KK217419.1, KK217424.1, KK217431.1, KK217434.1, KK217438.1, KK217443.1, KK217444.1, KK217446.1, KK217447.1, KK217453.1, KK217457.1, KK217458.1, KK217470.1, KK217472.1, KK217474.1, KK217478.1, KK217479.1, KK217486.1, KK217495.1, KK217507.1, KK217510.1, KK217523.1, KK217531.1, KK217540.1, KK217547.1, KK217551.1, KK217555.1, KK217558.1, KK217562.1, KK217571.1, KK217572.1, KK217574.1, KK217582.1, KK217586.1, KK217588.1, KK217590.1, KK217591.
ol1
## Hits object with 6906 hits and 0 metadata columns:
##          queryHits subjectHits
##          <integer>   <integer>
##      [1]         1       46314
##      [2]         2       51389
##      [3]         3       58239
##      [4]         4       32335
##      [5]         5       56687
##      ...       ...         ...
##   [6902]    111304       31864
##   [6903]    111332       13232
##   [6904]    111348       47105
##   [6905]    111360         774
##   [6906]    111427       40641
##   -------
##   queryLength: 111437 / subjectLength: 60897
CvLCpGislands <- dmrseqCvL[queryHits(ol1)]
my_CpGislandsol1 <- my_CpGislands[subjectHits(ol1)]
head(CvLCpGislands)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG19 10333007-10333692      * |        71  16.55967  0.576766
##   [2]       LG21 14273013-14273749      * |        81  14.61418  0.464748
##   [3] KK215293.1     186354-186845      * |        61   5.16072  0.391140
##   [4]       LG13 22015858-22016352      * |        82  14.22619  0.439795
##   [5] KK215283.1   1376211-1376895      * |       104  13.72310  0.361397
##   [6]       LG17   1251474-1251938      * |        61  12.56082 -0.401292
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]   18.9921 9.99999e-07  0.111437   8673138-8673208
##   [2]   15.3892 7.99999e-06  0.445748 11372899-11372979
##   [3]   12.1651 4.00000e-05  0.910330     296821-296881
##   [4]   11.5744 6.59999e-05  0.910330   4374338-4374419
##   [5]   11.5460 6.59999e-05  0.910330       56943-57046
##   [6]  -11.4403 7.09999e-05  0.910330   7069344-7069404
##   -------
##   seqinfo: 1180 sequences from an unspecified genome; no seqlengths
my_CpGislandsol1
## GRanges object with 6906 ranges and 2 metadata columns:
##            seqnames            ranges strand |   source             ID
##               <Rle>         <IRanges>  <Rle> | <factor>    <character>
##      [1]       LG19 10333012-10333278      + |  cpgplot      LG19.1464
##      [2]       LG21 14273253-14273572      + |  cpgplot      LG21.1424
##      [3] KK215293.1     186168-186505      + |  cpgplot  KK215293.1.65
##      [4]       LG13 22015853-22016336      + |  cpgplot      LG13.1407
##      [5] KK215283.1   1376061-1376879      + |  cpgplot KK215283.1.456
##      ...        ...               ...    ... .      ...            ...
##   [6902]       LG13 16655249-16655453      + |  cpgplot       LG13.936
##   [6903]        LG5 20090853-20091191      + |  cpgplot       LG5.1504
##   [6904]       LG19 20458688-20458935      + |  cpgplot      LG19.2255
##   [6905]        LG1   9750075-9750417      + |  cpgplot        LG1.774
##   [6906]       LG17   1992096-1992367      + |  cpgplot       LG17.225
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
CvLCpGislandsdf <- as.data.frame(CvLCpGislands,row.names = 1:nrow(as.data.frame(ranges(CvLCpGislands))))
str(CvLCpGislandsdf)
## 'data.frame':    6906 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1180 levels "KK215283.1","KK215284.1",..: 1168 1171 11 1162 1 1166 1179 1160 1169 1169 ...
##  $ start      : int  10333007 14273013 186354 22015858 1376211 1251474 18982718 14181818 16355666 16355666 ...
##  $ end        : int  10333692 14273749 186845 22016352 1376895 1251938 18983377 14182182 16355981 16355981 ...
##  $ width      : int  686 737 492 495 685 465 660 365 316 316 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  71 81 61 82 104 61 60 58 76 76 ...
##  $ area       : num  16.56 14.61 5.16 14.23 13.72 ...
##  $ beta       : num  0.577 0.465 0.391 0.44 0.361 ...
##  $ stat       : num  19 15.4 12.2 11.6 11.5 ...
##  $ pval       : num  1.0e-06 8.0e-06 4.0e-05 6.6e-05 6.6e-05 ...
##  $ qval       : num  0.111 0.446 0.91 0.91 0.91 ...
##  $ index.start: int  8673138 11372899 296821 4374338 56943 7069344 17405986 2836015 9599998 9599998 ...
##  $ index.end  : int  8673208 11372979 296881 4374419 57046 7069404 17406045 2836072 9600073 9600073 ...
##  $ index.width: int  71 81 61 82 104 61 60 58 76 76 ...
my_CpGislandsol1 <- as.data.frame(my_CpGislandsol1,row.names = 1:nrow(as.data.frame(ranges(my_CpGislandsol1))))
head(my_CpGislandsol1)
##     seqnames    start      end width strand  source             ID
## 1       LG19 10333012 10333278   267      + cpgplot      LG19.1464
## 2       LG21 14273253 14273572   320      + cpgplot      LG21.1424
## 3 KK215293.1   186168   186505   338      + cpgplot  KK215293.1.65
## 4       LG13 22015853 22016336   484      + cpgplot      LG13.1407
## 5 KK215283.1  1376061  1376879   819      + cpgplot KK215283.1.456
## 6       LG17  1251463  1251798   336      + cpgplot       LG17.120
CvLCpGislandsdf <- cbind(CvLCpGislandsdf,my_CpGislandsol1[c("source","ID")])
CvLCpGislandsdf$seqnames <- as.character(CvLCpGislandsdf$seqnames)
head(CvLCpGislandsdf)
##     seqnames    start      end width strand   L      area       beta      stat
## 1       LG19 10333007 10333692   686      *  71 16.559670  0.5767663  18.99209
## 2       LG21 14273013 14273749   737      *  81 14.614182  0.4647484  15.38915
## 3 KK215293.1   186354   186845   492      *  61  5.160722  0.3911403  12.16515
## 4       LG13 22015858 22016352   495      *  82 14.226193  0.4397952  11.57442
## 5 KK215283.1  1376211  1376895   685      * 104 13.723096  0.3613973  11.54604
## 6       LG17  1251474  1251938   465      *  61 12.560822 -0.4012925 -11.44033
##           pval      qval index.start index.end index.width  source
## 1 9.999990e-07 0.1114369     8673138   8673208          71 cpgplot
## 2 7.999992e-06 0.4457476    11372899  11372979          81 cpgplot
## 3 3.999996e-05 0.9103295      296821    296881          61 cpgplot
## 4 6.599993e-05 0.9103295     4374338   4374419          82 cpgplot
## 5 6.599993e-05 0.9103295       56943     57046         104 cpgplot
## 6 7.099993e-05 0.9103295     7069344   7069404          61 cpgplot
##               ID
## 1      LG19.1464
## 2      LG21.1424
## 3  KK215293.1.65
## 4      LG13.1407
## 5 KK215283.1.456
## 6       LG17.120
CvLCpGislandschrdf <- CvLCpGislandsdf[grep("LG",CvLCpGislandsdf$seqnames),]
head(CvLCpGislandschrdf)
##   seqnames    start      end width strand  L      area       beta      stat
## 1     LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 2     LG21 14273013 14273749   737      * 81 14.614182  0.4647484  15.38915
## 4     LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6     LG17  1251474  1251938   465      * 61 12.560822 -0.4012925 -11.44033
## 7      LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 8     LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
##           pval      qval index.start index.end index.width  source        ID
## 1 9.999990e-07 0.1114369     8673138   8673208          71 cpgplot LG19.1464
## 2 7.999992e-06 0.4457476    11372899  11372979          81 cpgplot LG21.1424
## 4 6.599993e-05 0.9103295     4374338   4374419          82 cpgplot LG13.1407
## 6 7.099993e-05 0.9103295     7069344   7069404          61 cpgplot  LG17.120
## 7 7.399993e-05 0.9103295    17405986  17406045          60 cpgplot  LG8.1584
## 8 8.099992e-05 0.9103295     2836015   2836072          58 cpgplot LG11.1123
CvLCpGislandschrdf <- CvLCpGislandschrdf[order(CvLCpGislandschrdf[,11]), ]
head(CvLCpGislandschrdf,10)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 2      LG21 14273013 14273749   737      * 81 14.614182  0.4647484  15.38915
## 4      LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6      LG17  1251474  1251938   465      * 61 12.560822 -0.4012925 -11.44033
## 7       LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 8      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
## 9       LG2 16355666 16355981   316      * 76  6.324347  0.3183476  10.87880
## 10      LG2 16355666 16355981   316      * 76  6.324347  0.3183476  10.87880
## 12     LG12 21371716 21372025   310      * 58  3.735525 -0.3274811 -10.48784
## 13     LG19  1188386  1188923   538      * 66 13.787455 -0.5147304 -10.45875
##            pval      qval index.start index.end index.width  source        ID
## 1  9.999990e-07 0.1114369     8673138   8673208          71 cpgplot LG19.1464
## 2  7.999992e-06 0.4457476    11372899  11372979          81 cpgplot LG21.1424
## 4  6.599993e-05 0.9103295     4374338   4374419          82 cpgplot LG13.1407
## 6  7.099993e-05 0.9103295     7069344   7069404          61 cpgplot  LG17.120
## 7  7.399993e-05 0.9103295    17405986  17406045          60 cpgplot  LG8.1584
## 8  8.099992e-05 0.9103295     2836015   2836072          58 cpgplot LG11.1123
## 9  1.009999e-04 0.9103295     9599998   9600073          76 cpgplot  LG2.1704
## 10 1.009999e-04 0.9103295     9599998   9600073          76 cpgplot  LG2.1705
## 12 1.389999e-04 0.9103295     3729020   3729077          58 cpgplot LG12.1498
## 13 1.399999e-04 0.9103295     8418295   8418360          66 cpgplot  LG19.359
rm(CvLCpGislands)
rm(CvLCpGislandsdf)
ol1 <- findOverlaps(dmrseqGvL,my_CpGislands)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215310.1, KK215370.1, KK215371.1, KK215372.1, KK215373.1, KK215378.1, KK215380.1, KK215381.1, KK215393.1, KK215396.1, KK215402.1, KK215404.1, KK215405.1, KK215406.1, KK215412.1, KK215417.1, KK215420.1, KK215421.1, KK215422.1, KK215423.1, KK215430.1, KK215433.1, KK215435.1, KK215437.1, KK215438.1, KK215440.1, KK215442.1, KK215456.1, KK215458.1, KK215461.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215468.1, KK215474.1, KK215480.1, KK215482.1, KK215483.1, KK215484.1, KK215485.1, KK215486.1, KK215487.1, KK215493.1, KK215494.1, KK215497.1, KK215498.1, KK215503.1, KK215504.1, KK215506.1, KK215508.1, KK215515.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215531.1, KK215533.1, KK215534.1, KK215536.1, KK215538.1, KK215541.1, KK215544.1, KK215545.1, KK215546.1, KK215548.1, KK215549.1, KK215551.1, KK215554.1, KK215557.1, KK215559.1, KK215560.1, KK215562.1, KK215565.1, KK215572.1, KK215573.1, KK215574.1, KK215577.1, KK215579.1, KK215580.1, KK215582.1, KK215584.1, KK215585.1, KK215591.1, KK215592.1, KK215593.1, KK215595.1, KK215598.1, KK215609.1, KK215612.1, KK215615.1, KK215620.1, KK215621.1, KK215625.1, KK215626.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215642.1, KK215643.1, KK215644.1, KK215645.1, KK215647.1, KK215649.1, KK215651.1, KK215652.1, KK215654.1, KK215656.1, KK215657.1, KK215661.1, KK215662.1, KK215663.1, KK215668.1, KK215671.1, KK215673.1, KK215675.1, KK215677.1, KK215684.1, KK215687.1, KK215688.1, KK215692.1, KK215695.1, KK215697.1, KK215698.1, KK215703.1, KK215705.1, KK215707.1, KK215708.1, KK215712.1, KK215715.1, KK215720.1, KK215721.1, KK215724.1, KK215727.1, KK215728.1, KK215730.1, KK215731.1, KK215734.1, KK215735.1, KK215736.1, KK215738.1, KK215743.1, KK215748.1, KK215756.1, KK215757.1, KK215761.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215786.1, KK215787.1, KK215789.1, KK215790.1, KK215798.1, KK215800.1, KK215802.1, KK215804.1, KK215808.1, KK215809.1, KK215810.1, KK215814.1, KK215816.1, KK215818.1, KK215824.1, KK215825.1, KK215834.1, KK215839.1, KK215842.1, KK215843.1, KK215844.1, KK215847.1, KK215849.1, KK215852.1, KK215857.1, KK215858.1, KK215859.1, KK215860.1, KK215864.1, KK215867.1, KK215870.1, KK215873.1, KK215881.1, KK215885.1, KK215886.1, KK215888.1, KK215890.1, KK215891.1, KK215893.1, KK215895.1, KK215897.1, KK215902.1, KK215905.1, KK215906.1, KK215908.1, KK215909.1, KK215911.1, KK215914.1, KK215915.1, KK215916.1, KK215918.1, KK215920.1, KK215921.1, KK215927.1, KK215928.1, KK215934.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215947.1, KK215949.1, KK215951.1, KK215952.1, KK215960.1, KK215961.1, KK215968.1, KK215969.1, KK215970.1, KK215972.1, KK215975.1, KK215976.1, KK215978.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215993.1, KK215997.1, KK216000.1, KK216012.1, KK216017.1, KK216029.1, KK216030.1, KK216033.1, KK216034.1, KK216035.1, KK216039.1, KK216041.1, KK216044.1, KK216048.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216063.1, KK216064.1, KK216069.1, KK216072.1, KK216075.1, KK216076.1, KK216077.1, KK216079.1, KK216085.1, KK216086.1, KK216087.1, KK216089.1, KK216092.1, KK216093.1, KK216100.1, KK216101.1, KK216106.1, KK216110.1, KK216114.1, KK216116.1, KK216120.1, KK216124.1, KK216128.1, KK216130.1, KK216131.1, KK216134.1, KK216135.1, KK216136.1, KK216140.1, KK216141.1, KK216142.1, KK216143.1, KK216147.1, KK216152.1, KK216157.1, KK216158.1, KK216163.1, KK216165.1, KK216168.1, KK216169.1, KK216171.1, KK216174.1, KK216176.1, KK216181.1, KK216184.1, KK216190.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216201.1, KK216202.1, KK216205.1, KK216212.1, KK216214.1, KK216215.1, KK216218.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216228.1, KK216230.1, KK216231.1, KK216234.1, KK216240.1, KK216241.1, KK216242.1, KK216245.1, KK216248.1, KK216253.1, KK216256.1, KK216258.1, KK216259.1, KK216261.1, KK216264.1, KK216266.1, KK216267.1, KK216269.1, KK216277.1, KK216278.1, KK216284.1, KK216287.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216294.1, KK216295.1, KK216304.1, KK216306.1, KK216307.1, KK216310.1, KK216313.1, KK216315.1, KK216317.1, KK216318.1, KK216319.1, KK216320.1, KK216324.1, KK216325.1, KK216329.1, KK216330.1, KK216332.1, KK216333.1, KK216336.1, KK216341.1, KK216342.1, KK216345.1, KK216351.1, KK216355.1, KK216361.1, KK216363.1, KK216369.1, KK216370.1, KK216374.1, KK216377.1, KK216380.1, KK216383.1, KK216387.1, KK216388.1, KK216390.1, KK216391.1, KK216393.1, KK216394.1, KK216396.1, KK216400.1, KK216402.1, KK216403.1, KK216404.1, KK216410.1, KK216418.1, KK216420.1, KK216423.1, KK216425.1, KK216427.1, KK216429.1, KK216430.1, KK216431.1, KK216437.1, KK216440.1, KK216442.1, KK216443.1, KK216454.1, KK216456.1, KK216458.1, KK216462.1, KK216465.1, KK216467.1, KK216476.1, KK216479.1, KK216486.1, KK216491.1, KK216492.1, KK216500.1, KK216502.1, KK216506.1, KK216508.1, KK216510.1, KK216511.1, KK216513.1, KK216515.1, KK216523.1, KK216526.1, KK216527.1, KK216530.1, KK216531.1, KK216534.1, KK216543.1, KK216551.1, KK216552.1, KK216559.1, KK216566.1, KK216571.1, KK216574.1, KK216584.1, KK216587.1, KK216596.1, KK216597.1, KK216598.1, KK216602.1, KK216603.1, KK216606.1, KK216619.1, KK216629.1, KK216630.1, KK216640.1, KK216643.1, KK216644.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216665.1, KK216668.1, KK216671.1, KK216674.1, KK216678.1, KK216679.1, KK216686.1, KK216688.1, KK216697.1, KK216702.1, KK216717.1, KK216725.1, KK216728.1, KK216731.1, KK216732.1, KK216733.1, KK216739.1, KK216745.1, KK216748.1, KK216767.1, KK216771.1, KK216774.1, KK216775.1, KK216782.1, KK216784.1, KK216795.1, KK216796.1, KK216807.1, KK216813.1, KK216814.1, KK216817.1, KK216823.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216866.1, KK216867.1, KK216870.1, KK216882.1, KK216884.1, KK216895.1, KK216896.1, KK216907.1, KK216908.1, KK216911.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216929.1, KK216934.1, KK216935.1, KK216936.1, KK216942.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216964.1, KK216965.1, KK216969.1, KK216971.1, KK216973.1, KK216977.1, KK216978.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216995.1, KK216998.1, KK216999.1, KK217001.1, KK217003.1, KK217007.1, KK217008.1, KK217010.1, KK217011.1, KK217012.1, KK217016.1, KK217017.1, KK217019.1, KK217021.1, KK217028.1, KK217032.1, KK217040.1, KK217045.1, KK217049.1, KK217059.1, KK217060.1, KK217063.1, KK217076.1, KK217077.1, KK217080.1, KK217083.1, KK217090.1, KK217091.1, KK217098.1, KK217100.1, KK217101.1, KK217104.1, KK217105.1, KK217120.1, KK217123.1, KK217128.1, KK217133.1, KK217135.1, KK217147.1, KK217151.1, KK217161.1, KK217163.1, KK217174.1, KK217179.1, KK217182.1, KK217186.1, KK217187.1, KK217193.1, KK217200.1, KK217203.1, KK217204.1, KK217206.1, KK217209.1, KK217223.1, KK217228.1, KK217233.1, KK217237.1, KK217238.1, KK217241.1, KK217242.1, KK217263.1, KK217265.1, KK217274.1, KK217276.1, KK217278.1, KK217280.1, KK217294.1, KK217295.1, KK217301.1, KK217303.1, KK217305.1, KK217313.1, KK217314.1, KK217323.1, KK217325.1, KK217345.1, KK217346.1, KK217347.1, KK217352.1, KK217360.1, KK217367.1, KK217369.1, KK217372.1, KK217375.1, KK217381.1, KK217382.1, KK217395.1, KK217402.1, KK217406.1, KK217409.1, KK217414.1, KK217417.1, KK217419.1, KK217420.1, KK217422.1, KK217424.1, KK217427.1, KK217431.1, KK217437.1, KK217442.1, KK217444.1, KK217445.1, KK217446.1, KK217447.1, KK217452.1, KK217461.1, KK217462.1, KK217470.1, KK217474.1, KK217475.1, KK217481.1, KK217484.1, KK217485.1, KK217490.1, KK217492.1, KK217497.1, KK217499.1, KK217531.1, KK217532.1, KK217534.1, KK217538.1, KK217540.1, KK217541.1, KK217545.1, KK217551.1, KK217559.1, KK217562.1, KK217571.1, KK217574.1, KK217582.1, KK217584.1, KK217585.1, KK217588.1, KK217591.1, KK217596.1, KK217598.1, KK217602.1, KK217607.1, KK217610.1, KK217612.1, KK217613.1, KK217618.1, KK217619.1, KK217625.1, KK217630.1, KK217632.1, KK217635.1, KK217638.1, KK217640.1, KK217644.1, KK217651.1, KK217652.1, KK217656.
ol1
## Hits object with 5133 hits and 0 metadata columns:
##          queryHits subjectHits
##          <integer>   <integer>
##      [1]         1       28631
##      [2]         2       56687
##      [3]         3       48988
##      [4]         4        1612
##      [5]         6       32069
##      ...       ...         ...
##   [5129]     91454       41415
##   [5130]     91465       20788
##   [5131]     91489       38403
##   [5132]     91494       47546
##   [5133]     91515       28729
##   -------
##   queryLength: 91524 / subjectLength: 60897
GvLCpGislands <- dmrseqGvL[queryHits(ol1)]
my_CpGislandsol1 <- my_CpGislands[subjectHits(ol1)]
head(GvLCpGislands)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG11 28461237-28461741      * |       108  11.63697 -0.277374
##   [2] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [3]       LG20 17269425-17270374      * |        73  10.41376  0.475571
##   [4]        LG1 22240537-22241922      * |        78   8.68085  0.351599
##   [5]       LG13 18160946-18161831      * |        95  16.31186 -0.397064
##   [6] KK215287.1     944627-944828      * |        36   4.29946 -0.458437
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]  -16.2750 7.14404e-06  0.653851   3678849-3678956
##   [2]   15.2345 1.78601e-05  0.749204       65611-65766
##   [3]   14.5876 2.50041e-05  0.749204 12375529-12375601
##   [4]   13.2709 4.64363e-05  0.749204   1550715-1550792
##   [5]  -12.7574 5.59616e-05  0.749204   4929871-4929965
##   [6]  -12.6832 6.07243e-05  0.749204     223719-223754
##   -------
##   seqinfo: 1169 sequences from an unspecified genome; no seqlengths
my_CpGislandsol1
## GRanges object with 5133 ranges and 2 metadata columns:
##            seqnames            ranges strand |   source             ID
##               <Rle>         <IRanges>  <Rle> | <factor>    <character>
##      [1]       LG11 28461223-28461750      + |  cpgplot      LG11.2496
##      [2] KK215283.1   1376061-1376879      + |  cpgplot KK215283.1.456
##      [3]       LG20 17270266-17270490      + |  cpgplot      LG20.1278
##      [4]        LG1 22240830-22241036      + |  cpgplot       LG1.1612
##      [5]       LG13 18160935-18161432      + |  cpgplot      LG13.1141
##      ...        ...               ...    ... .      ...            ...
##   [5129]       LG17 11272216-11272425      + |  cpgplot       LG17.999
##   [5130]        LG8 23526042-23526320      + |  cpgplot       LG8.2088
##   [5131]       LG16   2070386-2070612      + |  cpgplot       LG16.501
##   [5132]       LG19 25355604-25355803      + |  cpgplot      LG19.2696
##   [5133]       LG11 28762243-28763456      + |  cpgplot      LG11.2594
##   -------
##   seqinfo: 646 sequences from an unspecified genome; no seqlengths
GvLCpGislandsdf <- as.data.frame(GvLCpGislands,row.names = 1:nrow(as.data.frame(ranges(GvLCpGislands))))
str(GvLCpGislands)
## Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
##   ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
##   .. .. ..@ values         : Factor w/ 1169 levels "KK215283.1","KK215284.1",..: 1149 1 1159 1147 1151 5 1149 24 1165 1154 ...
##   .. .. ..@ lengths        : int [1:4810] 1 1 1 1 1 1 1 1 1 1 ...
##   .. .. ..@ elementMetadata: NULL
##   .. .. ..@ metadata       : list()
##   ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
##   .. .. ..@ start          : int [1:5133] 28461237 1376121 17269425 22240537 18160946 944627 10041760 101373 2971274 508971 ...
##   .. .. ..@ width          : int [1:5133] 505 779 950 1386 886 202 376 715 272 981 ...
##   .. .. ..@ NAMES          : NULL
##   .. .. ..@ elementType    : chr "ANY"
##   .. .. ..@ elementMetadata: NULL
##   .. .. ..@ metadata       : list()
##   ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
##   .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 3
##   .. .. ..@ lengths        : int 5133
##   .. .. ..@ elementMetadata: NULL
##   .. .. ..@ metadata       : list()
##   ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
##   .. .. ..@ seqnames   : chr [1:1169] "KK215283.1" "KK215284.1" "KK215285.1" "KK215286.1" ...
##   .. .. ..@ seqlengths : int [1:1169] NA NA NA NA NA NA NA NA NA NA ...
##   .. .. ..@ is_circular: logi [1:1169] NA NA NA NA NA NA ...
##   .. .. ..@ genome     : chr [1:1169] NA NA NA NA ...
##   ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
##   .. .. ..@ rownames       : NULL
##   .. .. ..@ nrows          : int 5133
##   .. .. ..@ listData       :List of 7
##   .. .. .. ..$ L    : int [1:5133] 108 156 73 78 95 36 75 68 58 88 ...
##   .. .. .. ..$ area : num [1:5133] 11.64 18.41 10.41 8.68 16.31 ...
##   .. .. .. ..$ beta : num [1:5133] -0.277 0.329 0.476 0.352 -0.397 ...
##   .. .. .. ..$ stat : num [1:5133] -16.3 15.2 14.6 13.3 -12.8 ...
##   .. .. .. ..$ pval : num [1:5133] 7.14e-06 1.79e-05 2.50e-05 4.64e-05 5.60e-05 ...
##   .. .. .. ..$ qval : num [1:5133] 0.654 0.749 0.749 0.749 0.749 ...
##   .. .. .. ..$ index:Formal class 'IRanges' [package "IRanges"] with 6 slots
##   .. .. .. .. .. ..@ start          : int [1:5133] 3678849 65611 12375529 1550715 4929871 223719 3123427 479142 16775120 7140119 ...
##   .. .. .. .. .. ..@ width          : int [1:5133] 108 156 73 78 95 36 75 68 58 88 ...
##   .. .. .. .. .. ..@ NAMES          : NULL
##   .. .. .. .. .. ..@ elementType    : chr "ANY"
##   .. .. .. .. .. ..@ elementMetadata: NULL
##   .. .. .. .. .. ..@ metadata       : list()
##   .. .. ..@ elementType    : chr "ANY"
##   .. .. ..@ elementMetadata: NULL
##   .. .. ..@ metadata       : list()
##   ..@ elementType    : chr "ANY"
##   ..@ metadata       : list()
my_CpGislandsol1 <- as.data.frame(my_CpGislandsol1,row.names = 1:nrow(as.data.frame(ranges(my_CpGislandsol1))))
head(my_CpGislandsol1)
##     seqnames    start      end width strand  source             ID
## 1       LG11 28461223 28461750   528      + cpgplot      LG11.2496
## 2 KK215283.1  1376061  1376879   819      + cpgplot KK215283.1.456
## 3       LG20 17270266 17270490   225      + cpgplot      LG20.1278
## 4        LG1 22240830 22241036   207      + cpgplot       LG1.1612
## 5       LG13 18160935 18161432   498      + cpgplot      LG13.1141
## 6 KK215287.1   944612   944830   219      + cpgplot KK215287.1.200
GvLCpGislandsdf <- cbind(GvLCpGislandsdf,my_CpGislandsol1[c("source","ID")])
GvLCpGislandsdf$seqnames <- as.character(GvLCpGislandsdf$seqnames)
head(GvLCpGislandsdf)
##     seqnames    start      end width strand   L      area       beta      stat
## 1       LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 2 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 3       LG20 17269425 17270374   950      *  73 10.413759  0.4755714  14.58765
## 4        LG1 22240537 22241922  1386      *  78  8.680847  0.3515985  13.27092
## 5       LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 6 KK215287.1   944627   944828   202      *  36  4.299457 -0.4584372 -12.68316
##           pval      qval index.start index.end index.width  source
## 1 7.144039e-06 0.6538511     3678849   3678956         108 cpgplot
## 2 1.786010e-05 0.7492043       65611     65766         156 cpgplot
## 3 2.500414e-05 0.7492043    12375529  12375601          73 cpgplot
## 4 4.643626e-05 0.7492043     1550715   1550792          78 cpgplot
## 5 5.596164e-05 0.7492043     4929871   4929965          95 cpgplot
## 6 6.072433e-05 0.7492043      223719    223754          36 cpgplot
##               ID
## 1      LG11.2496
## 2 KK215283.1.456
## 3      LG20.1278
## 4       LG1.1612
## 5      LG13.1141
## 6 KK215287.1.200
GvLCpGislandschrdf <- GvLCpGislandsdf[grep("LG",GvLCpGislandsdf$seqnames),]
head(GvLCpGislandschrdf)
##   seqnames    start      end width strand   L      area       beta      stat
## 1     LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 3     LG20 17269425 17270374   950      *  73 10.413759  0.4755714  14.58765
## 4      LG1 22240537 22241922  1386      *  78  8.680847  0.3515985  13.27092
## 5     LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7     LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9      LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##           pval      qval index.start index.end index.width  source        ID
## 1 7.144039e-06 0.6538511     3678849   3678956         108 cpgplot LG11.2496
## 3 2.500414e-05 0.7492043    12375529  12375601          73 cpgplot LG20.1278
## 4 4.643626e-05 0.7492043     1550715   1550792          78 cpgplot  LG1.1612
## 5 5.596164e-05 0.7492043     4929871   4929965          95 cpgplot LG13.1141
## 7 6.548703e-05 0.7492043     3123427   3123501          75 cpgplot  LG11.699
## 9 9.287251e-05 0.7879743    16775120  16775177          58 cpgplot   LG5.532
GvLCpGislandschrdf <- GvLCpGislandschrdf[order(GvLCpGislandschrdf[,11]), ]
head(GvLCpGislandschrdf,10)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 3      LG20 17269425 17270374   950      *  73 10.413759  0.4755714  14.58765
## 4       LG1 22240537 22241922  1386      *  78  8.680847  0.3515985  13.27092
## 5      LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7      LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10     LG16   508971   509951   981      *  88 14.089129 -0.3991232 -11.83323
## 12     LG17  4434405  4435108   704      *  67 10.629923 -0.4174846 -11.47364
## 13      LG5 19662076 19662488   413      *  46  3.595347  0.3130988  11.43112
## 14      LG3 31400775 31402677  1903      *  73 10.270659  0.3407376  11.36557
##            pval      qval index.start index.end index.width  source        ID
## 1  7.144039e-06 0.6538511     3678849   3678956         108 cpgplot LG11.2496
## 3  2.500414e-05 0.7492043    12375529  12375601          73 cpgplot LG20.1278
## 4  4.643626e-05 0.7492043     1550715   1550792          78 cpgplot  LG1.1612
## 5  5.596164e-05 0.7492043     4929871   4929965          95 cpgplot LG13.1141
## 7  6.548703e-05 0.7492043     3123427   3123501          75 cpgplot  LG11.699
## 9  9.287251e-05 0.7879743    16775120  16775177          58 cpgplot   LG5.532
## 10 1.059699e-04 0.7879743     7140119   7140206          88 cpgplot  LG16.165
## 12 1.357367e-04 0.7879743     8251105   8251171          67 cpgplot  LG17.545
## 13 1.357367e-04 0.7879743    17222347  17222392          46 cpgplot  LG5.1484
## 14 1.464528e-04 0.7879743    15649137  15649209          73 cpgplot  LG3.1584
rm(GvLCpGislands)
rm(GvLCpGislandsdf)

dmrs annotated to promoter regions

ol1 <- findOverlaps(dmrseqCvG,my_Promoters)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215341.1, KK215360.1, KK215378.1, KK215383.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215415.1, KK215418.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215440.1, KK215441.1, KK215443.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215454.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215472.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215501.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215547.1, KK215548.1, KK215549.1, KK215551.1, KK215556.1, KK215558.1, KK215559.1, KK215560.1, KK215561.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215581.1, KK215583.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215589.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215620.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215627.1, KK215628.1, KK215629.1, KK215630.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215639.1, KK215641.1, KK215642.1, KK215645.1, KK215646.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215664.1, KK215665.1, KK215668.1, KK215669.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215683.1, KK215684.1, KK215688.1, KK215692.1, KK215695.1, KK215700.1, KK215701.1, KK215703.1, KK215704.1, KK215705.1, KK215706.1, KK215709.1, KK215710.1, KK215711.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215724.1, KK215726.1, KK215727.1, KK215728.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215741.1, KK215742.1, KK215743.1, KK215745.1, KK215750.1, KK215752.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215762.1, KK215763.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215779.1, KK215780.1, KK215782.1, KK215783.1, KK215785.1, KK215786.1, KK215788.1, KK215789.1, KK215792.1, KK215794.1, KK215795.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215815.1, KK215816.1, KK215821.1, KK215825.1, KK215827.1, KK215832.1, KK215834.1, KK215836.1, KK215837.1, KK215838.1, KK215843.1, KK215848.1, KK215849.1, KK215854.1, KK215857.1, KK215858.1, KK215859.1, KK215861.1, KK215863.1, KK215864.1, KK215872.1, KK215873.1, KK215875.1, KK215877.1, KK215878.1, KK215880.1, KK215881.1, KK215882.1, KK215885.1, KK215886.1, KK215890.1, KK215891.1, KK215894.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215907.1, KK215909.1, KK215910.1, KK215911.1, KK215914.1, KK215915.1, KK215918.1, KK215921.1, KK215922.1, KK215923.1, KK215928.1, KK215929.1, KK215934.1, KK215935.1, KK215937.1, KK215942.1, KK215943.1, KK215945.1, KK215946.1, KK215949.1, KK215951.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215962.1, KK215965.1, KK215967.1, KK215969.1, KK215970.1, KK215973.1, KK215974.1, KK215976.1, KK215977.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215990.1, KK215993.1, KK215994.1, KK215997.1, KK215999.1, KK216000.1, KK216001.1, KK216012.1, KK216015.1, KK216017.1, KK216018.1, KK216021.1, KK216023.1, KK216025.1, KK216026.1, KK216028.1, KK216029.1, KK216030.1, KK216032.1, KK216033.1, KK216034.1, KK216035.1, KK216037.1, KK216038.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216049.1, KK216053.1, KK216063.1, KK216064.1, KK216065.1, KK216066.1, KK216067.1, KK216068.1, KK216069.1, KK216070.1, KK216071.1, KK216072.1, KK216074.1, KK216075.1, KK216076.1, KK216079.1, KK216082.1, KK216084.1, KK216085.1, KK216086.1, KK216089.1, KK216093.1, KK216094.1, KK216097.1, KK216099.1, KK216102.1, KK216103.1, KK216109.1, KK216111.1, KK216114.1, KK216118.1, KK216120.1, KK216122.1, KK216124.1, KK216128.1, KK216133.1, KK216134.1, KK216135.1, KK216141.1, KK216142.1, KK216143.1, KK216150.1, KK216152.1, KK216155.1, KK216157.1, KK216158.1, KK216165.1, KK216166.1, KK216169.1, KK216171.1, KK216172.1, KK216173.1, KK216174.1, KK216175.1, KK216177.1, KK216180.1, KK216184.1, KK216186.1, KK216190.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216200.1, KK216203.1, KK216208.1, KK216212.1, KK216213.1, KK216215.1, KK216219.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216229.1, KK216232.1, KK216236.1, KK216237.1, KK216238.1, KK216240.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216259.1, KK216260.1, KK216261.1, KK216264.1, KK216266.1, KK216270.1, KK216273.1, KK216275.1, KK216278.1, KK216280.1, KK216281.1, KK216282.1, KK216284.1, KK216285.1, KK216287.1, KK216289.1, KK216290.1, KK216295.1, KK216303.1, KK216306.1, KK216310.1, KK216313.1, KK216320.1, KK216322.1, KK216323.1, KK216324.1, KK216325.1, KK216326.1, KK216329.1, KK216330.1, KK216331.1, KK216334.1, KK216336.1, KK216341.1, KK216342.1, KK216351.1, KK216359.1, KK216360.1, KK216363.1, KK216364.1, KK216366.1, KK216368.1, KK216370.1, KK216371.1, KK216377.1, KK216383.1, KK216384.1, KK216389.1, KK216391.1, KK216394.1, KK216396.1, KK216402.1, KK216404.1, KK216405.1, KK216408.1, KK216410.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216423.1, KK216428.1, KK216432.1, KK216433.1, KK216436.1, KK216438.1, KK216440.1, KK216442.1, KK216445.1, KK216447.1, KK216451.1, KK216452.1, KK216453.1, KK216456.1, KK216457.1, KK216458.1, KK216462.1, KK216468.1, KK216477.1, KK216482.1, KK216492.1, KK216502.1, KK216504.1, KK216506.1, KK216507.1, KK216508.1, KK216510.1, KK216511.1, KK216512.1, KK216513.1, KK216514.1, KK216515.1, KK216519.1, KK216523.1, KK216526.1, KK216530.1, KK216531.1, KK216538.1, KK216540.1, KK216548.1, KK216552.1, KK216553.1, KK216556.1, KK216569.1, KK216571.1, KK216572.1, KK216574.1, KK216576.1, KK216592.1, KK216599.1, KK216606.1, KK216607.1, KK216610.1, KK216615.1, KK216627.1, KK216638.1, KK216640.1, KK216647.1, KK216651.1, KK216657.1, KK216661.1, KK216665.1, KK216672.1, KK216674.1, KK216678.1, KK216680.1, KK216685.1, KK216691.1, KK216695.1, KK216709.1, KK216712.1, KK216714.1, KK216716.1, KK216717.1, KK216725.1, KK216726.1, KK216732.1, KK216737.1, KK216740.1, KK216745.1, KK216746.1, KK216748.1, KK216752.1, KK216758.1, KK216763.1, KK216773.1, KK216779.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216800.1, KK216804.1, KK216811.1, KK216814.1, KK216815.1, KK216817.1, KK216830.1, KK216831.1, KK216834.1, KK216842.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216863.1, KK216865.1, KK216867.1, KK216870.1, KK216873.1, KK216879.1, KK216881.1, KK216887.1, KK216896.1, KK216898.1, KK216899.1, KK216903.1, KK216905.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216922.1, KK216923.1, KK216930.1, KK216931.1, KK216934.1, KK216942.1, KK216943.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216963.1, KK216964.1, KK216965.1, KK216968.1, KK216971.1, KK216973.1, KK216974.1, KK216975.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216999.1, KK217000.1, KK217001.1, KK217002.1, KK217003.1, KK217007.1, KK217012.1, KK217019.1, KK217032.1, KK217037.1, KK217059.1, KK217063.1, KK217065.1, KK217066.1, KK217072.1, KK217074.1, KK217076.1, KK217077.1, KK217079.1, KK217082.1, KK217083.1, KK217086.1, KK217088.1, KK217093.1, KK217098.1, KK217101.1, KK217103.1, KK217105.1, KK217109.1, KK217111.1, KK217112.1, KK217114.1, KK217117.1, KK217119.1, KK217120.1, KK217121.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217135.1, KK217140.1, KK217146.1, KK217147.1, KK217182.
ol1
## Hits object with 14102 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         7        3392
##       [2]         8       33428
##       [3]         8       33427
##       [4]        14       16453
##       [5]        18       10110
##       ...       ...         ...
##   [14098]    110742       18462
##   [14099]    110742       18464
##   [14100]    110756       29534
##   [14101]    110756       29535
##   [14102]    110769       33461
##   -------
##   queryLength: 110780 / subjectLength: 34314
CvGpromoters <- dmrseqCvG[queryHits(ol1)]
myPromotersol1 <- my_Promoters[subjectHits(ol1)]
head(CvGpromoters)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]        LG5   2971274-2971545      * |        61   8.49567  0.378574
##   [2] KK215283.1     934758-935340      * |        78   5.69451  0.335720
##   [3] KK215283.1     934758-935340      * |        78   5.69451  0.335720
##   [4] KK215297.1       56283-56546      * |        39   3.74232 -0.390374
##   [5]       LG11 10641658-10642177      * |        56   6.75082  0.402875
##   [6]        LG4   4685116-4685638      * |        91  11.17036  0.288880
##            stat        pval      qval             index
##       <numeric>   <numeric> <numeric>         <IRanges>
##   [1]   11.6533 6.44251e-05  0.719377 14903599-14903659
##   [2]   11.2804 8.44919e-05  0.719377       37410-37487
##   [3]   11.2804 8.44919e-05  0.719377       37410-37487
##   [4]  -10.8012 1.27794e-04  0.719377     339662-339700
##   [5]   10.6969 1.32019e-04  0.719377   2790037-2790092
##   [6]   10.6179 1.39412e-04  0.719377 14118347-14118437
##   -------
##   seqinfo: 1181 sequences from an unspecified genome; no seqlengths
myPromotersol1
## GRanges object with 14102 ranges and 3 metadata columns:
##             seqnames            ranges strand |                 V5
##                <Rle>         <IRanges>  <Rle> |        <character>
##       [1]        LG5   2969966-2972967      + | ENSPREG00000022867
##       [2] KK215283.1     934210-937211      - | ENSPREG00000018359
##       [3] KK215283.1     934974-937975      - | ENSPREG00000018359
##       [4] KK215297.1       54834-57835      + | ENSPREG00000015292
##       [5]       LG11 10640186-10643187      + | ENSPREG00000001606
##       ...        ...               ...    ... .                ...
##   [14098]        LG3 25503964-25506965      - | ENSPREG00000007085
##   [14099]        LG3 25504550-25507551      - | ENSPREG00000007085
##   [14100]        LG8 11492118-11495119      - | ENSPREG00000001025
##   [14101]        LG8 11493215-11496216      - | ENSPREG00000001157
##   [14102] KK215284.1     497405-500406      - | ENSPREG00000002312
##                           V6              V7
##                  <character>     <character>
##       [1] ENSPRET00000034154          asb14a
##       [2] ENSPRET00000027444         tbc1d30
##       [3] ENSPRET00000027444         tbc1d30
##       [4] ENSPRET00000023016           ube2c
##       [5] ENSPRET00000002349 uncharacterised
##       ...                ...             ...
##   [14098] ENSPRET00000010508           adcy7
##   [14099] ENSPRET00000010598           adcy7
##   [14100] ENSPRET00000001572 uncharacterised
##   [14101] ENSPRET00000001592 uncharacterised
##   [14102] ENSPRET00000003263           med31
##   -------
##   seqinfo: 452 sequences from an unspecified genome; no seqlengths
CvGpromotersdf <- as.data.frame(CvGpromoters,row.names = 1:nrow(as.data.frame(ranges(CvGpromoters))))
str(CvGpromotersdf)
## 'data.frame':    14102 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1181 levels "KK215283.1","KK215284.1",..: 1177 1 1 15 1161 1176 1159 1164 1177 735 ...
##  $ start      : int  2971274 934758 934758 56283 10641658 4685116 17896682 9176317 561500 1683 ...
##  $ end        : int  2971545 935340 935340 56546 10642177 4685638 17897364 9177886 562079 2330 ...
##  $ width      : int  272 583 583 264 520 523 683 1570 580 648 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  61 78 78 39 56 91 78 117 58 82 ...
##  $ area       : num  8.5 5.69 5.69 3.74 6.75 ...
##  $ beta       : num  0.379 0.336 0.336 -0.39 0.403 ...
##  $ stat       : num  11.7 11.3 11.3 -10.8 10.7 ...
##  $ pval       : num  6.44e-05 8.45e-05 8.45e-05 1.28e-04 1.32e-04 ...
##  $ qval       : num  0.719 0.719 0.719 0.719 0.719 ...
##  $ index.start: int  14903599 37410 37410 339662 2790037 14118347 1269169 4982092 14828919 753522 ...
##  $ index.end  : int  14903659 37487 37487 339700 2790092 14118437 1269246 4982208 14828976 753603 ...
##  $ index.width: int  61 78 78 39 56 91 78 117 58 82 ...
myPromotersoldf1 <- as.data.frame(myPromotersol1,row.names = 1:nrow(as.data.frame(ranges(myPromotersol1))))
head(myPromotersoldf1)
##     seqnames    start      end width strand                 V5
## 1        LG5  2969966  2972967  3002      + ENSPREG00000022867
## 2 KK215283.1   934210   937211  3002      - ENSPREG00000018359
## 3 KK215283.1   934974   937975  3002      - ENSPREG00000018359
## 4 KK215297.1    54834    57835  3002      + ENSPREG00000015292
## 5       LG11 10640186 10643187  3002      + ENSPREG00000001606
## 6        LG4  4683335  4686336  3002      + ENSPREG00000003007
##                   V6              V7
## 1 ENSPRET00000034154          asb14a
## 2 ENSPRET00000027444         tbc1d30
## 3 ENSPRET00000027444         tbc1d30
## 4 ENSPRET00000023016           ube2c
## 5 ENSPRET00000002349 uncharacterised
## 6 ENSPRET00000004307 uncharacterised
CvGpromotersdf <- cbind(CvGpromotersdf,myPromotersoldf1[c("V5","V6","V7")])
CvGpromotersdf$seqnames <- as.character(CvGpromotersdf$seqnames)
head(CvGpromotersdf)
##     seqnames    start      end width strand  L      area       beta      stat
## 1        LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 2 KK215283.1   934758   935340   583      * 78  5.694514  0.3357201  11.28039
## 3 KK215283.1   934758   935340   583      * 78  5.694514  0.3357201  11.28039
## 4 KK215297.1    56283    56546   264      * 39  3.742322 -0.3903736 -10.80117
## 5       LG11 10641658 10642177   520      * 56  6.750824  0.4028755  10.69685
## 6        LG4  4685116  4685638   523      * 91 11.170358  0.2888801  10.61794
##           pval      qval index.start index.end index.width                 V5
## 1 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 2 8.449193e-05 0.7193775       37410     37487          78 ENSPREG00000018359
## 3 8.449193e-05 0.7193775       37410     37487          78 ENSPREG00000018359
## 4 1.277940e-04 0.7193775      339662    339700          39 ENSPREG00000015292
## 5 1.320186e-04 0.7193775     2790037   2790092          56 ENSPREG00000001606
## 6 1.394117e-04 0.7193775    14118347  14118437          91 ENSPREG00000003007
##                   V6              V7
## 1 ENSPRET00000034154          asb14a
## 2 ENSPRET00000027444         tbc1d30
## 3 ENSPRET00000027444         tbc1d30
## 4 ENSPRET00000023016           ube2c
## 5 ENSPRET00000002349 uncharacterised
## 6 ENSPRET00000004307 uncharacterised
CvGpromoterschrdf <- CvGpromotersdf[grep("LG",CvGpromotersdf$seqnames),]
head(CvGpromoterschrdf)
##   seqnames    start      end width strand   L      area       beta       stat
## 1      LG5  2971274  2971545   272      *  61  8.495669  0.3785743  11.653334
## 5     LG11 10641658 10642177   520      *  56  6.750824  0.4028755  10.696852
## 6      LG4  4685116  4685638   523      *  91 11.170358  0.2888801  10.617941
## 7      LG1 17896682 17897364   683      *  78  7.067168 -0.4086131 -10.417264
## 8     LG14  9176317  9177886  1570      * 117 12.973315 -0.2718633  -9.972136
## 9      LG5   561500   562079   580      *  58  4.402356 -0.3328806  -9.438165
##           pval      qval index.start index.end index.width                 V5
## 1 0.0000644251 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 5 0.0001320186 0.7193775     2790037   2790092          56 ENSPREG00000001606
## 6 0.0001394117 0.7193775    14118347  14118437          91 ENSPREG00000003007
## 7 0.0001700400 0.7193775     1269169   1269246          78 ENSPREG00000004582
## 8 0.0002365774 0.7193775     4982092   4982208         117 ENSPREG00000021264
## 9 0.0003844383 0.7193775    14828919  14828976          58 ENSPREG00000021434
##                   V6              V7
## 1 ENSPRET00000034154          asb14a
## 5 ENSPRET00000002349 uncharacterised
## 6 ENSPRET00000004307 uncharacterised
## 7 ENSPRET00000006703 uncharacterised
## 8 ENSPRET00000031741          ppm1nb
## 9 ENSPRET00000031993            GRM7
CvGpromoterschrdf <- CvGpromoterschrdf[order(CvGpromoterschrdf[,11]), ]
colnames(CvGpromoterschrdf) <- c("seqnames","start","end","width","strand","L","area", "beta","stat", "pvalue","qvalue","index.start", "index.width","L", "gene_id","transcript_id", "gene_name")
head(CvGpromoterschrdf,20)
##    seqnames    start      end width strand   L      area       beta       stat
## 1       LG5  2971274  2971545   272      *  61  8.495669  0.3785743  11.653334
## 5      LG11 10641658 10642177   520      *  56  6.750824  0.4028755  10.696852
## 6       LG4  4685116  4685638   523      *  91 11.170358  0.2888801  10.617941
## 7       LG1 17896682 17897364   683      *  78  7.067168 -0.4086131 -10.417264
## 8      LG14  9176317  9177886  1570      * 117 12.973315 -0.2718633  -9.972136
## 9       LG5   561500   562079   580      *  58  4.402356 -0.3328806  -9.438165
## 11     LG11 28397337 28398020   684      *  79  4.496291 -0.2993888  -9.354211
## 12     LG18  3020876  3021389   514      *  56  4.151694 -0.3258269  -9.316115
## 13     LG18  3020876  3021389   514      *  56  4.151694 -0.3258269  -9.316115
## 14      LG9 29010586 29010947   362      *  37  2.114055 -0.3274617  -9.312339
## 15     LG13 32607789 32608770   982      *  49  4.473201 -0.2909705  -9.299812
## 16     LG13 32607789 32608770   982      *  49  4.473201 -0.2909705  -9.299812
## 17     LG13 32607789 32608770   982      *  49  4.473201 -0.2909705  -9.299812
## 18      LG3 10040979 10041557   579      *  41  7.104433  0.4191580   9.242021
## 19      LG6 27375910 27376342   433      *  72  4.189514 -0.2413977  -9.242003
## 20     LG15 30357859 30358677   819      * 116  7.688326 -0.2033232  -9.216736
## 21     LG15 30357859 30358677   819      * 116  7.688326 -0.2033232  -9.216736
## 22     LG13 18419150 18419602   453      *  54  6.885688 -0.3786169  -9.120724
## 23     LG13 18419150 18419602   453      *  54  6.885688 -0.3786169  -9.120724
## 24     LG22  8861308  8862891  1584      *  92 11.836798 -0.3396811  -9.086127
##          pvalue    qvalue index.start index.width   L            gene_id
## 1  0.0000644251 0.7193775    14903599    14903659  61 ENSPREG00000022867
## 5  0.0001320186 0.7193775     2790037     2790092  56 ENSPREG00000001606
## 6  0.0001394117 0.7193775    14118347    14118437  91 ENSPREG00000003007
## 7  0.0001700400 0.7193775     1269169     1269246  78 ENSPREG00000004582
## 8  0.0002365774 0.7193775     4982092     4982208 117 ENSPREG00000021264
## 9  0.0003844383 0.7193775    14828919    14828976  58 ENSPREG00000021434
## 11 0.0004034490 0.7193775     3259562     3259640  79 ENSPREG00000009968
## 12 0.0004150666 0.7193775     8030468     8030523  56 ENSPREG00000000773
## 13 0.0004150666 0.7193775     8030468     8030523  56 ENSPREG00000000773
## 14 0.0004150666 0.7193775    18758558    18758594  37 ENSPREG00000010392
## 15 0.0004214035 0.7193775     4748898     4748946  49 ENSPREG00000020974
## 16 0.0004214035 0.7193775     4748898     4748946  49 ENSPREG00000020974
## 17 0.0004214035 0.7193775     4748898     4748946  49 ENSPREG00000020974
## 18 0.0004478072 0.7193775    13428876    13428916  41 ENSPREG00000018896
## 19 0.0004478072 0.7193775    16366428    16366499  72 ENSPREG00000015822
## 20 0.0004573126 0.7193775     6309589     6309704 116 ENSPREG00000013474
## 21 0.0004573126 0.7193775     6309589     6309704 116 ENSPREG00000013474
## 22 0.0005016708 0.7193775     4381929     4381982  54 ENSPREG00000001609
## 23 0.0005016708 0.7193775     4381929     4381982  54 ENSPREG00000001609
## 24 0.0005164569 0.7193775    12175632    12175723  92 ENSPREG00000015260
##         transcript_id       gene_name
## 1  ENSPRET00000034154          asb14a
## 5  ENSPRET00000002349 uncharacterised
## 6  ENSPRET00000004307 uncharacterised
## 7  ENSPRET00000006703 uncharacterised
## 8  ENSPRET00000031741          ppm1nb
## 9  ENSPRET00000031993            GRM7
## 11 ENSPRET00000014921           meaf6
## 12 ENSPRET00000001034 uncharacterised
## 13 ENSPRET00000001034 uncharacterised
## 14 ENSPRET00000015598       tbc1d10aa
## 15 ENSPRET00000031555 uncharacterised
## 16 ENSPRET00000031521 uncharacterised
## 17 ENSPRET00000031485 uncharacterised
## 18 ENSPRET00000028232        slc27a2a
## 19 ENSPRET00000023704           nptna
## 20 ENSPRET00000020140 uncharacterised
## 21 ENSPRET00000020129 uncharacterised
## 22 ENSPRET00000002207           SH2B2
## 23 ENSPRET00000002207           SH2B2
## 24 ENSPRET00000022840 uncharacterised
rm(CvGpromoters)
rm(CvGpromotersdf)
ol1 <- findOverlaps(dmrseqCvL,my_Promoters)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215351.1, KK215360.1, KK215378.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215412.1, KK215414.1, KK215415.1, KK215418.1, KK215420.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215441.1, KK215443.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215454.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215472.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215501.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215512.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215526.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215546.1, KK215547.1, KK215553.1, KK215554.1, KK215556.1, KK215558.1, KK215559.1, KK215560.1, KK215561.1, KK215562.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215581.1, KK215582.1, KK215583.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215602.1, KK215603.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215627.1, KK215628.1, KK215629.1, KK215630.1, KK215632.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215639.1, KK215641.1, KK215642.1, KK215646.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215665.1, KK215668.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215683.1, KK215688.1, KK215692.1, KK215700.1, KK215701.1, KK215703.1, KK215704.1, KK215705.1, KK215706.1, KK215707.1, KK215709.1, KK215710.1, KK215711.1, KK215712.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215723.1, KK215724.1, KK215726.1, KK215727.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215741.1, KK215742.1, KK215748.1, KK215750.1, KK215752.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215758.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215780.1, KK215782.1, KK215783.1, KK215785.1, KK215788.1, KK215789.1, KK215792.1, KK215794.1, KK215795.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215816.1, KK215819.1, KK215825.1, KK215827.1, KK215832.1, KK215834.1, KK215838.1, KK215839.1, KK215840.1, KK215841.1, KK215842.1, KK215843.1, KK215849.1, KK215857.1, KK215860.1, KK215861.1, KK215863.1, KK215864.1, KK215870.1, KK215875.1, KK215878.1, KK215881.1, KK215885.1, KK215886.1, KK215891.1, KK215894.1, KK215896.1, KK215897.1, KK215898.1, KK215900.1, KK215903.1, KK215907.1, KK215908.1, KK215909.1, KK215911.1, KK215915.1, KK215917.1, KK215918.1, KK215920.1, KK215921.1, KK215923.1, KK215927.1, KK215928.1, KK215929.1, KK215934.1, KK215935.1, KK215937.1, KK215938.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215949.1, KK215951.1, KK215952.1, KK215953.1, KK215956.1, KK215957.1, KK215960.1, KK215962.1, KK215965.1, KK215969.1, KK215970.1, KK215971.1, KK215972.1, KK215973.1, KK215974.1, KK215976.1, KK215978.1, KK215979.1, KK215983.1, KK215989.1, KK215990.1, KK215993.1, KK215995.1, KK215997.1, KK215999.1, KK216000.1, KK216001.1, KK216006.1, KK216008.1, KK216012.1, KK216015.1, KK216017.1, KK216021.1, KK216023.1, KK216026.1, KK216027.1, KK216030.1, KK216032.1, KK216036.1, KK216037.1, KK216038.1, KK216039.1, KK216040.1, KK216041.1, KK216044.1, KK216048.1, KK216049.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216064.1, KK216065.1, KK216068.1, KK216069.1, KK216071.1, KK216072.1, KK216074.1, KK216075.1, KK216076.1, KK216079.1, KK216080.1, KK216082.1, KK216083.1, KK216084.1, KK216087.1, KK216094.1, KK216096.1, KK216097.1, KK216103.1, KK216106.1, KK216109.1, KK216110.1, KK216111.1, KK216112.1, KK216114.1, KK216115.1, KK216118.1, KK216128.1, KK216131.1, KK216135.1, KK216140.1, KK216141.1, KK216143.1, KK216146.1, KK216150.1, KK216159.1, KK216162.1, KK216164.1, KK216165.1, KK216166.1, KK216168.1, KK216171.1, KK216174.1, KK216175.1, KK216176.1, KK216177.1, KK216181.1, KK216184.1, KK216190.1, KK216192.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216200.1, KK216202.1, KK216203.1, KK216206.1, KK216208.1, KK216212.1, KK216213.1, KK216214.1, KK216215.1, KK216219.1, KK216225.1, KK216226.1, KK216227.1, KK216229.1, KK216231.1, KK216232.1, KK216234.1, KK216235.1, KK216237.1, KK216241.1, KK216244.1, KK216245.1, KK216251.1, KK216253.1, KK216254.1, KK216256.1, KK216258.1, KK216259.1, KK216263.1, KK216264.1, KK216265.1, KK216266.1, KK216267.1, KK216272.1, KK216273.1, KK216275.1, KK216278.1, KK216280.1, KK216285.1, KK216287.1, KK216288.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216295.1, KK216304.1, KK216308.1, KK216310.1, KK216316.1, KK216317.1, KK216319.1, KK216320.1, KK216322.1, KK216323.1, KK216324.1, KK216325.1, KK216329.1, KK216341.1, KK216342.1, KK216345.1, KK216347.1, KK216351.1, KK216359.1, KK216364.1, KK216366.1, KK216369.1, KK216370.1, KK216379.1, KK216384.1, KK216385.1, KK216386.1, KK216387.1, KK216388.1, KK216389.1, KK216391.1, KK216392.1, KK216393.1, KK216394.1, KK216396.1, KK216402.1, KK216403.1, KK216404.1, KK216405.1, KK216414.1, KK216418.1, KK216420.1, KK216422.1, KK216430.1, KK216431.1, KK216433.1, KK216436.1, KK216437.1, KK216438.1, KK216440.1, KK216443.1, KK216447.1, KK216452.1, KK216456.1, KK216457.1, KK216462.1, KK216467.1, KK216477.1, KK216486.1, KK216491.1, KK216492.1, KK216498.1, KK216499.1, KK216503.1, KK216504.1, KK216506.1, KK216507.1, KK216511.1, KK216512.1, KK216520.1, KK216523.1, KK216530.1, KK216534.1, KK216538.1, KK216540.1, KK216556.1, KK216558.1, KK216570.1, KK216571.1, KK216572.1, KK216574.1, KK216586.1, KK216592.1, KK216595.1, KK216598.1, KK216604.1, KK216606.1, KK216609.1, KK216611.1, KK216615.1, KK216618.1, KK216622.1, KK216627.1, KK216630.1, KK216638.1, KK216641.1, KK216645.1, KK216646.1, KK216647.1, KK216648.1, KK216649.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216674.1, KK216685.1, KK216688.1, KK216696.1, KK216697.1, KK216704.1, KK216705.1, KK216707.1, KK216709.1, KK216710.1, KK216716.1, KK216717.1, KK216721.1, KK216723.1, KK216725.1, KK216726.1, KK216733.1, KK216737.1, KK216739.1, KK216740.1, KK216746.1, KK216747.1, KK216748.1, KK216752.1, KK216761.1, KK216763.1, KK216764.1, KK216767.1, KK216780.1, KK216782.1, KK216784.1, KK216792.1, KK216796.1, KK216803.1, KK216807.1, KK216815.1, KK216817.1, KK216820.1, KK216830.1, KK216841.1, KK216842.1, KK216846.1, KK216847.1, KK216851.1, KK216852.1, KK216865.1, KK216867.1, KK216868.1, KK216870.1, KK216871.1, KK216879.1, KK216880.1, KK216884.1, KK216887.1, KK216895.1, KK216902.1, KK216905.1, KK216908.1, KK216912.1, KK216914.1, KK216918.1, KK216921.1, KK216922.1, KK216930.1, KK216931.1, KK216932.1, KK216945.1, KK216953.1, KK216957.1, KK216968.1, KK216969.1, KK216970.1, KK216971.1, KK216974.1, KK216978.1, KK216980.1, KK216989.1, KK216990.1, KK216994.1, KK216995.1, KK217000.1, KK217002.1, KK217007.1, KK217008.1, KK217012.1, KK217014.1, KK217016.1, KK217019.1, KK217023.1, KK217024.1, KK217026.1, KK217040.1, KK217049.1, KK217053.1, KK217059.1, KK217063.1, KK217064.1, KK217065.1, KK217066.1, KK217068.1, KK217073.1, KK217076.1, KK217079.1, KK217082.1, KK217083.1, KK217088.1, KK217093.1, KK217095.1, KK217098.1, KK217100.1, KK217103.1, KK217104.1, KK217105.1, KK217111.1, KK217112.1, KK217114.1, KK217120.1, KK217123.1, KK217126.1, KK217128.1, KK217130.1, KK217132.1, KK217133.1, KK217135.1, KK217137.1, KK217139.1, KK217140.1, KK217149.1, KK217150.1, KK217154.1, KK217160.
ol1
## Hits object with 13757 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         3       33702
##       [2]         3       16350
##       [3]         5       16084
##       [4]         5       33437
##       [5]         5       16085
##       ...       ...         ...
##   [13753]    111375       16027
##   [13754]    111406       25648
##   [13755]    111412        5082
##   [13756]    111415       30673
##   [13757]    111419        9810
##   -------
##   queryLength: 111437 / subjectLength: 34314
CvLpromoters <- dmrseqCvL[queryHits(ol1)]
myPromotersol1 <- my_Promoters[subjectHits(ol1)]
head(CvLpromoters)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames          ranges strand |         L      area      beta
##            <Rle>       <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1] KK215293.1   186354-186845      * |        61   5.16072  0.391140
##   [2] KK215293.1   186354-186845      * |        61   5.16072  0.391140
##   [3] KK215283.1 1376211-1376895      * |       104  13.72310  0.361397
##   [4] KK215283.1 1376211-1376895      * |       104  13.72310  0.361397
##   [5] KK215283.1 1376211-1376895      * |       104  13.72310  0.361397
##   [6] KK215283.1 1376211-1376895      * |       104  13.72310  0.361397
##            stat        pval      qval         index
##       <numeric>   <numeric> <numeric>     <IRanges>
##   [1]   12.1651 4.00000e-05   0.91033 296821-296881
##   [2]   12.1651 4.00000e-05   0.91033 296821-296881
##   [3]   11.5460 6.59999e-05   0.91033   56943-57046
##   [4]   11.5460 6.59999e-05   0.91033   56943-57046
##   [5]   11.5460 6.59999e-05   0.91033   56943-57046
##   [6]   11.5460 6.59999e-05   0.91033   56943-57046
##   -------
##   seqinfo: 1180 sequences from an unspecified genome; no seqlengths
myPromotersol1
## GRanges object with 13757 ranges and 3 metadata columns:
##             seqnames            ranges strand |                 V5
##                <Rle>         <IRanges>  <Rle> |        <character>
##       [1] KK215293.1     184306-187307      - | ENSPREG00000013483
##       [2] KK215293.1     186237-189238      + | ENSPREG00000013500
##       [3] KK215283.1   1375383-1378384      + | ENSPREG00000019522
##       [4] KK215283.1   1375391-1378392      - | ENSPREG00000019483
##       [5] KK215283.1   1375441-1378442      + | ENSPREG00000019522
##       ...        ...               ...    ... .                ...
##   [13753]       LG23 17233490-17236491      + | ENSPREG00000017022
##   [13754]        LG7 27300001-27303002      - | ENSPREG00000021367
##   [13755]       LG16 11055885-11058886      + | ENSPREG00000007507
##   [13756]       LG12 20232878-20235879      - | ENSPREG00000017960
##   [13757]       LG15 25203599-25206600      + | ENSPREG00000007341
##                           V6              V7
##                  <character>     <character>
##       [1] ENSPRET00000020133 uncharacterised
##       [2] ENSPRET00000020155 uncharacterised
##       [3] ENSPRET00000029315           calua
##       [4] ENSPRET00000029113            sco2
##       [5] ENSPRET00000029364           calua
##       ...                ...             ...
##   [13753] ENSPRET00000025534            net1
##   [13754] ENSPRET00000031896 uncharacterised
##   [13755] ENSPRET00000011125 uncharacterised
##   [13756] ENSPRET00000026838           oacyl
##   [13757] ENSPRET00000010865 uncharacterised
##   -------
##   seqinfo: 452 sequences from an unspecified genome; no seqlengths
CvLpromotersdf <- as.data.frame(CvLpromoters,row.names = 1:nrow(as.data.frame(ranges(CvLpromoters))))
str(CvLpromotersdf)
## 'data.frame':    13757 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1180 levels "KK215283.1","KK215284.1",..: 11 11 1 1 1 1 1160 1160 1165 1165 ...
##  $ start      : int  186354 186354 1376211 1376211 1376211 1376211 14181818 14181818 852906 852906 ...
##  $ end        : int  186845 186845 1376895 1376895 1376895 1376895 14182182 14182182 853242 853242 ...
##  $ width      : int  492 492 685 685 685 685 365 365 337 337 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  61 61 104 104 104 104 58 58 59 59 ...
##  $ area       : num  5.16 5.16 13.72 13.72 13.72 ...
##  $ beta       : num  0.391 0.391 0.361 0.361 0.361 ...
##  $ stat       : num  12.2 12.2 11.5 11.5 11.5 ...
##  $ pval       : num  4.0e-05 4.0e-05 6.6e-05 6.6e-05 6.6e-05 ...
##  $ qval       : num  0.91 0.91 0.91 0.91 0.91 ...
##  $ index.start: int  296821 296821 56943 56943 56943 56943 2836015 2836015 6214834 6214834 ...
##  $ index.end  : int  296881 296881 57046 57046 57046 57046 2836072 2836072 6214892 6214892 ...
##  $ index.width: int  61 61 104 104 104 104 58 58 59 59 ...
myPromotersoldf1 <- as.data.frame(myPromotersol1,row.names = 1:nrow(as.data.frame(ranges(myPromotersol1))))
head(myPromotersoldf1)
##     seqnames   start     end width strand                 V5                 V6
## 1 KK215293.1  184306  187307  3002      - ENSPREG00000013483 ENSPRET00000020133
## 2 KK215293.1  186237  189238  3002      + ENSPREG00000013500 ENSPRET00000020155
## 3 KK215283.1 1375383 1378384  3002      + ENSPREG00000019522 ENSPRET00000029315
## 4 KK215283.1 1375391 1378392  3002      - ENSPREG00000019483 ENSPRET00000029113
## 5 KK215283.1 1375441 1378442  3002      + ENSPREG00000019522 ENSPRET00000029364
## 6 KK215283.1 1376555 1379556  3002      + ENSPREG00000019522 ENSPRET00000029379
##                V7
## 1 uncharacterised
## 2 uncharacterised
## 3           calua
## 4            sco2
## 5           calua
## 6           calua
CvLpromotersdf <- cbind(CvLpromotersdf,myPromotersoldf1[c("V5","V6","V7")])
CvLpromotersdf$seqnames <- as.character(CvLpromotersdf$seqnames)
head(CvLpromotersdf)
##     seqnames   start     end width strand   L      area      beta     stat
## 1 KK215293.1  186354  186845   492      *  61  5.160722 0.3911403 12.16515
## 2 KK215293.1  186354  186845   492      *  61  5.160722 0.3911403 12.16515
## 3 KK215283.1 1376211 1376895   685      * 104 13.723096 0.3613973 11.54604
## 4 KK215283.1 1376211 1376895   685      * 104 13.723096 0.3613973 11.54604
## 5 KK215283.1 1376211 1376895   685      * 104 13.723096 0.3613973 11.54604
## 6 KK215283.1 1376211 1376895   685      * 104 13.723096 0.3613973 11.54604
##           pval      qval index.start index.end index.width                 V5
## 1 3.999996e-05 0.9103295      296821    296881          61 ENSPREG00000013483
## 2 3.999996e-05 0.9103295      296821    296881          61 ENSPREG00000013500
## 3 6.599993e-05 0.9103295       56943     57046         104 ENSPREG00000019522
## 4 6.599993e-05 0.9103295       56943     57046         104 ENSPREG00000019483
## 5 6.599993e-05 0.9103295       56943     57046         104 ENSPREG00000019522
## 6 6.599993e-05 0.9103295       56943     57046         104 ENSPREG00000019522
##                   V6              V7
## 1 ENSPRET00000020133 uncharacterised
## 2 ENSPRET00000020155 uncharacterised
## 3 ENSPRET00000029315           calua
## 4 ENSPRET00000029113            sco2
## 5 ENSPRET00000029364           calua
## 6 ENSPRET00000029379           calua
CvLpromoterschrdf <- CvLpromotersdf[grep("LG",CvLpromotersdf$seqnames),]
head(CvLpromoterschrdf)
##    seqnames    start      end width strand  L      area       beta       stat
## 7      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.253784
## 8      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.253784
## 9      LG16   852906   853242   337      * 59  5.256405 -0.3099585 -10.146571
## 10     LG16   852906   853242   337      * 59  5.256405 -0.3099585 -10.146571
## 11     LG16   852906   853242   337      * 59  5.256405 -0.3099585 -10.146571
## 12      LG4  4685053  4685638   586      * 95 13.510971  0.3158647   9.507047
##            pval      qval index.start index.end index.width                 V5
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 9  1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 10 1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 11 1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 12 3.109997e-04 0.9103295    13816123  13816217          95 ENSPREG00000003007
##                    V6              V7
## 7  ENSPRET00000011036 uncharacterised
## 8  ENSPRET00000011036 uncharacterised
## 9  ENSPRET00000023555 uncharacterised
## 10 ENSPRET00000023563 uncharacterised
## 11 ENSPRET00000023563 uncharacterised
## 12 ENSPRET00000004307 uncharacterised
CvLpromoterschrdf <- CvLpromoterschrdf[order(CvLpromoterschrdf[,11]), ]
colnames(CvGpromoterschrdf) <- c("seqnames","start","end","width","strand","L","area", "beta","stat", "pvalue","qvalue","index.start", "index.width","L", "gene_id","transcript_id", "gene_name")
head(CvLpromoterschrdf,20)
##    seqnames    start      end width strand   L      area       beta       stat
## 7      LG11 14181818 14182182   365      *  58  4.745863 -0.3570840 -11.253784
## 8      LG11 14181818 14182182   365      *  58  4.745863 -0.3570840 -11.253784
## 9      LG16   852906   853242   337      *  59  5.256405 -0.3099585 -10.146571
## 10     LG16   852906   853242   337      *  59  5.256405 -0.3099585 -10.146571
## 11     LG16   852906   853242   337      *  59  5.256405 -0.3099585 -10.146571
## 12      LG4  4685053  4685638   586      *  95 13.510971  0.3158647   9.507047
## 13      LG1 18070269 18071303  1035      *  89  8.962426 -0.2763986  -9.401986
## 14     LG23  1376882  1377608   727      *  61  8.986266 -0.4336691  -8.975553
## 15      LG7 18259264 18260110   847      *  28  6.708446  0.5276226   8.971170
## 18      LG7 17085665 17086479   815      * 101 13.436313  0.3494188   8.758125
## 19      LG2 36596343 36596990   648      *  50  3.500546 -0.2395078  -8.623741
## 20      LG5 24679174 24679587   414      *  45  5.861411  0.4044968   8.612346
## 21      LG7 19972809 19973456   648      *  29  5.172946  0.5530375   8.610610
## 22      LG7 19972809 19973456   648      *  29  5.172946  0.5530375   8.610610
## 23      LG9  9489130  9489710   581      *  42  4.072473 -0.3281138  -8.589622
## 24      LG9  9489130  9489710   581      *  42  4.072473 -0.3281138  -8.589622
## 26     LG11 10184557 10185539   983      * 120 11.815863  0.3049973   8.354479
## 27      LG3 19963040 19963388   349      *  26  2.761796 -0.4410081  -8.328988
## 28     LG18  4888241  4889449  1209      * 100 13.786780 -0.3311130  -8.323026
## 29     LG13  1652733  1653376   644      *  31  3.668329  0.4171294   8.204332
##            pval      qval index.start index.end index.width                 V5
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 9  1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 10 1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 11 1.839998e-04 0.9103295     6214834   6214892          59 ENSPREG00000015724
## 12 3.109997e-04 0.9103295    13816123  13816217          95 ENSPREG00000003007
## 13 3.399997e-04 0.9103295     1243346   1243434          89 ENSPREG00000005128
## 14 4.889995e-04 0.9103295    12382860  12382920          61 ENSPREG00000022413
## 15 4.909995e-04 0.9103295    16597659  16597686          28 ENSPREG00000003617
## 18 6.069994e-04 0.9261309    16563951  16564051         101 ENSPREG00000001520
## 19 6.929993e-04 0.9405804    10087471  10087520          50 ENSPREG00000013239
## 20 6.969993e-04 0.9405804    15117287  15117331          45 ENSPREG00000012853
## 21 6.979993e-04 0.9405804    16636303  16636331          29 ENSPREG00000006394
## 22 6.979993e-04 0.9405804    16636303  16636331          29 ENSPREG00000006394
## 23 7.089993e-04 0.9405804    17896665  17896706          42 ENSPREG00000003150
## 24 7.089993e-04 0.9405804    17896665  17896706          42 ENSPREG00000003150
## 26 8.829991e-04 0.9532280     2714240   2714359         120 ENSPREG00000021725
## 27 9.109991e-04 0.9532280    13367667  13367692          26 ENSPREG00000000589
## 28 9.189991e-04 0.9532280     7897415   7897514         100 ENSPREG00000004844
## 29 1.033999e-03 0.9532280     3888789   3888819          31 ENSPREG00000008830
##                    V6              V7
## 7  ENSPRET00000011036 uncharacterised
## 8  ENSPRET00000011036 uncharacterised
## 9  ENSPRET00000023555 uncharacterised
## 10 ENSPRET00000023563 uncharacterised
## 11 ENSPRET00000023563 uncharacterised
## 12 ENSPRET00000004307 uncharacterised
## 13 ENSPRET00000007557         slc25a4
## 14 ENSPRET00000033466          ppfia2
## 15 ENSPRET00000005305           uts2a
## 18 ENSPRET00000002091      zgc:198371
## 19 ENSPRET00000019775           lims2
## 20 ENSPRET00000019215       ankrd33ab
## 21 ENSPRET00000009531          asic1a
## 22 ENSPRET00000009545          asic1a
## 23 ENSPRET00000004527          prdm8b
## 24 ENSPRET00000004527          prdm8b
## 26 ENSPRET00000032420          hoxa5a
## 27 ENSPRET00000001109          nedd4a
## 28 ENSPRET00000007125 uncharacterised
## 29 ENSPRET00000013202 uncharacterised
rm(CvLpromoters)
rm(CvLpromotersdf)
ol1 <- findOverlaps(dmrseqGvL,my_Promoters)
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': KK215332.1, KK215339.1, KK215341.1, KK215360.1, KK215378.1, KK215387.1, KK215391.1, KK215393.1, KK215395.1, KK215396.1, KK215400.1, KK215401.1, KK215402.1, KK215405.1, KK215406.1, KK215407.1, KK215408.1, KK215411.1, KK215412.1, KK215415.1, KK215418.1, KK215420.1, KK215421.1, KK215424.1, KK215427.1, KK215430.1, KK215432.1, KK215433.1, KK215435.1, KK215439.1, KK215440.1, KK215441.1, KK215444.1, KK215446.1, KK215448.1, KK215451.1, KK215453.1, KK215455.1, KK215456.1, KK215459.1, KK215462.1, KK215463.1, KK215465.1, KK215466.1, KK215467.1, KK215474.1, KK215475.1, KK215479.1, KK215480.1, KK215482.1, KK215484.1, KK215485.1, KK215486.1, KK215488.1, KK215490.1, KK215491.1, KK215492.1, KK215494.1, KK215496.1, KK215497.1, KK215498.1, KK215502.1, KK215503.1, KK215504.1, KK215506.1, KK215507.1, KK215508.1, KK215511.1, KK215513.1, KK215514.1, KK215515.1, KK215516.1, KK215517.1, KK215518.1, KK215519.1, KK215521.1, KK215523.1, KK215524.1, KK215525.1, KK215528.1, KK215529.1, KK215530.1, KK215531.1, KK215533.1, KK215538.1, KK215540.1, KK215541.1, KK215543.1, KK215544.1, KK215545.1, KK215546.1, KK215548.1, KK215549.1, KK215551.1, KK215553.1, KK215554.1, KK215559.1, KK215560.1, KK215561.1, KK215562.1, KK215567.1, KK215568.1, KK215573.1, KK215574.1, KK215577.1, KK215578.1, KK215579.1, KK215581.1, KK215582.1, KK215583.1, KK215584.1, KK215585.1, KK215586.1, KK215587.1, KK215588.1, KK215589.1, KK215590.1, KK215594.1, KK215595.1, KK215597.1, KK215598.1, KK215601.1, KK215602.1, KK215603.1, KK215605.1, KK215606.1, KK215608.1, KK215615.1, KK215616.1, KK215620.1, KK215621.1, KK215624.1, KK215625.1, KK215626.1, KK215628.1, KK215629.1, KK215630.1, KK215632.1, KK215633.1, KK215634.1, KK215635.1, KK215636.1, KK215637.1, KK215638.1, KK215639.1, KK215641.1, KK215642.1, KK215644.1, KK215645.1, KK215647.1, KK215649.1, KK215652.1, KK215654.1, KK215655.1, KK215657.1, KK215658.1, KK215661.1, KK215662.1, KK215663.1, KK215664.1, KK215668.1, KK215669.1, KK215670.1, KK215671.1, KK215672.1, KK215673.1, KK215675.1, KK215677.1, KK215678.1, KK215684.1, KK215688.1, KK215692.1, KK215695.1, KK215699.1, KK215700.1, KK215701.1, KK215703.1, KK215705.1, KK215706.1, KK215707.1, KK215709.1, KK215711.1, KK215712.1, KK215715.1, KK215719.1, KK215720.1, KK215721.1, KK215722.1, KK215724.1, KK215726.1, KK215727.1, KK215728.1, KK215733.1, KK215734.1, KK215736.1, KK215737.1, KK215738.1, KK215739.1, KK215743.1, KK215745.1, KK215748.1, KK215750.1, KK215753.1, KK215754.1, KK215755.1, KK215756.1, KK215757.1, KK215762.1, KK215763.1, KK215764.1, KK215765.1, KK215767.1, KK215768.1, KK215769.1, KK215770.1, KK215771.1, KK215772.1, KK215775.1, KK215776.1, KK215777.1, KK215778.1, KK215782.1, KK215783.1, KK215786.1, KK215788.1, KK215789.1, KK215792.1, KK215797.1, KK215798.1, KK215802.1, KK215804.1, KK215807.1, KK215810.1, KK215812.1, KK215814.1, KK215816.1, KK215818.1, KK215821.1, KK215825.1, KK215834.1, KK215836.1, KK215839.1, KK215842.1, KK215843.1, KK215847.1, KK215849.1, KK215852.1, KK215857.1, KK215858.1, KK215859.1, KK215860.1, KK215864.1, KK215867.1, KK215870.1, KK215872.1, KK215873.1, KK215877.1, KK215881.1, KK215885.1, KK215886.1, KK215890.1, KK215891.1, KK215893.1, KK215894.1, KK215897.1, KK215902.1, KK215905.1, KK215907.1, KK215908.1, KK215909.1, KK215910.1, KK215911.1, KK215914.1, KK215915.1, KK215917.1, KK215918.1, KK215920.1, KK215921.1, KK215927.1, KK215928.1, KK215929.1, KK215934.1, KK215938.1, KK215941.1, KK215942.1, KK215943.1, KK215945.1, KK215946.1, KK215949.1, KK215951.1, KK215952.1, KK215960.1, KK215965.1, KK215967.1, KK215969.1, KK215970.1, KK215972.1, KK215974.1, KK215975.1, KK215976.1, KK215977.1, KK215978.1, KK215979.1, KK215982.1, KK215983.1, KK215984.1, KK215987.1, KK215993.1, KK215995.1, KK215997.1, KK215999.1, KK216000.1, KK216012.1, KK216017.1, KK216021.1, KK216023.1, KK216029.1, KK216030.1, KK216033.1, KK216034.1, KK216035.1, KK216038.1, KK216039.1, KK216041.1, KK216044.1, KK216048.1, KK216050.1, KK216053.1, KK216056.1, KK216059.1, KK216063.1, KK216064.1, KK216067.1, KK216069.1, KK216072.1, KK216075.1, KK216076.1, KK216077.1, KK216079.1, KK216085.1, KK216086.1, KK216087.1, KK216089.1, KK216093.1, KK216094.1, KK216095.1, KK216099.1, KK216106.1, KK216109.1, KK216110.1, KK216114.1, KK216115.1, KK216120.1, KK216124.1, KK216128.1, KK216131.1, KK216134.1, KK216135.1, KK216140.1, KK216141.1, KK216142.1, KK216143.1, KK216150.1, KK216152.1, KK216157.1, KK216158.1, KK216162.1, KK216163.1, KK216165.1, KK216168.1, KK216169.1, KK216171.1, KK216174.1, KK216176.1, KK216177.1, KK216181.1, KK216184.1, KK216190.1, KK216192.1, KK216193.1, KK216194.1, KK216195.1, KK216197.1, KK216198.1, KK216201.1, KK216202.1, KK216203.1, KK216205.1, KK216212.1, KK216213.1, KK216214.1, KK216215.1, KK216217.1, KK216218.1, KK216219.1, KK216222.1, KK216225.1, KK216226.1, KK216227.1, KK216231.1, KK216234.1, KK216235.1, KK216236.1, KK216240.1, KK216241.1, KK216242.1, KK216245.1, KK216248.1, KK216253.1, KK216256.1, KK216258.1, KK216259.1, KK216261.1, KK216264.1, KK216265.1, KK216266.1, KK216267.1, KK216269.1, KK216273.1, KK216278.1, KK216282.1, KK216284.1, KK216285.1, KK216287.1, KK216289.1, KK216290.1, KK216291.1, KK216292.1, KK216293.1, KK216295.1, KK216303.1, KK216304.1, KK216306.1, KK216307.1, KK216310.1, KK216313.1, KK216315.1, KK216316.1, KK216317.1, KK216318.1, KK216319.1, KK216320.1, KK216323.1, KK216324.1, KK216325.1, KK216326.1, KK216329.1, KK216330.1, KK216331.1, KK216333.1, KK216336.1, KK216341.1, KK216342.1, KK216345.1, KK216351.1, KK216361.1, KK216363.1, KK216368.1, KK216369.1, KK216370.1, KK216374.1, KK216377.1, KK216383.1, KK216387.1, KK216388.1, KK216390.1, KK216391.1, KK216393.1, KK216394.1, KK216396.1, KK216400.1, KK216402.1, KK216403.1, KK216404.1, KK216410.1, KK216418.1, KK216420.1, KK216423.1, KK216427.1, KK216429.1, KK216430.1, KK216431.1, KK216437.1, KK216440.1, KK216442.1, KK216443.1, KK216447.1, KK216454.1, KK216456.1, KK216458.1, KK216462.1, KK216465.1, KK216467.1, KK216476.1, KK216478.1, KK216485.1, KK216486.1, KK216491.1, KK216492.1, KK216498.1, KK216499.1, KK216500.1, KK216502.1, KK216506.1, KK216507.1, KK216508.1, KK216510.1, KK216511.1, KK216513.1, KK216515.1, KK216523.1, KK216526.1, KK216527.1, KK216530.1, KK216531.1, KK216534.1, KK216543.1, KK216552.1, KK216559.1, KK216566.1, KK216571.1, KK216574.1, KK216584.1, KK216596.1, KK216598.1, KK216602.1, KK216603.1, KK216606.1, KK216629.1, KK216630.1, KK216636.1, KK216638.1, KK216640.1, KK216643.1, KK216644.1, KK216648.1, KK216650.1, KK216652.1, KK216657.1, KK216661.1, KK216665.1, KK216668.1, KK216671.1, KK216674.1, KK216678.1, KK216679.1, KK216686.1, KK216688.1, KK216696.1, KK216697.1, KK216702.1, KK216717.1, KK216725.1, KK216728.1, KK216731.1, KK216732.1, KK216733.1, KK216739.1, KK216745.1, KK216748.1, KK216767.1, KK216771.1, KK216774.1, KK216775.1, KK216782.1, KK216784.1, KK216795.1, KK216796.1, KK216804.1, KK216807.1, KK216811.1, KK216813.1, KK216814.1, KK216817.1, KK216823.1, KK216841.1, KK216848.1, KK216852.1, KK216859.1, KK216861.1, KK216866.1, KK216867.1, KK216870.1, KK216881.1, KK216882.1, KK216884.1, KK216892.1, KK216895.1, KK216896.1, KK216907.1, KK216908.1, KK216911.1, KK216912.1, KK216913.1, KK216914.1, KK216921.1, KK216929.1, KK216934.1, KK216935.1, KK216936.1, KK216942.1, KK216945.1, KK216946.1, KK216950.1, KK216954.1, KK216957.1, KK216959.1, KK216964.1, KK216965.1, KK216969.1, KK216971.1, KK216973.1, KK216977.1, KK216978.1, KK216980.1, KK216987.1, KK216988.1, KK216994.1, KK216995.1, KK216998.1, KK216999.1, KK217001.1, KK217003.1, KK217007.1, KK217008.1, KK217010.1, KK217011.1, KK217012.1, KK217016.1, KK217017.1, KK217019.1, KK217021.1, KK217032.1, KK217040.1, KK217049.1, KK217059.1, KK217063.1, KK217076.1, KK217077.1, KK217080.1, KK217083.1, KK217090.1, KK217091.1, KK217098.1, KK217100.1, KK217101.1, KK217104.1, KK217105.1, KK217111.1, KK217120.1, KK217123.1, KK217128.1, KK217133.1, KK217135.1, KK217147.1, KK217151.1, KK217161.1, KK217163.1, KK217174.1, KK217179.1, KK217182.1, KK217183.1, KK217186.1, KK217187.1, KK217189.1, KK217190.1, KK217193.1, KK217200.1, KK217203.1, KK217204.1, KK217206.1, KK217209.1, KK217228.1, KK217233.1, KK217237.1, KK217238.
ol1
## Hits object with 11399 hits and 0 metadata columns:
##           queryHits subjectHits
##           <integer>   <integer>
##       [1]         1       10594
##       [2]         2       16084
##       [3]         2       33437
##       [4]         2       16085
##       [5]         2       16086
##       ...       ...         ...
##   [11395]     91501        7318
##   [11396]     91501        7319
##   [11397]     91503       27731
##   [11398]     91509       29991
##   [11399]     91521       24112
##   -------
##   queryLength: 91524 / subjectLength: 34314
GvLpromoters <- dmrseqGvL[queryHits(ol1)]
myPromotersol1 <- my_Promoters[subjectHits(ol1)]
head(GvLpromoters)
## GRanges object with 6 ranges and 7 metadata columns:
##         seqnames            ranges strand |         L      area      beta
##            <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
##   [1]       LG11 28461237-28461741      * |       108  11.63697 -0.277374
##   [2] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [3] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [4] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [5] KK215283.1   1376121-1376899      * |       156  18.40713  0.329127
##   [6] KK215306.1     101373-102087      * |        68   9.62665  0.432490
##            stat        pval      qval           index
##       <numeric>   <numeric> <numeric>       <IRanges>
##   [1]  -16.2750 7.14404e-06  0.653851 3678849-3678956
##   [2]   15.2345 1.78601e-05  0.749204     65611-65766
##   [3]   15.2345 1.78601e-05  0.749204     65611-65766
##   [4]   15.2345 1.78601e-05  0.749204     65611-65766
##   [5]   15.2345 1.78601e-05  0.749204     65611-65766
##   [6]   12.3753 7.62031e-05  0.774935   479142-479209
##   -------
##   seqinfo: 1169 sequences from an unspecified genome; no seqlengths
myPromotersol1
## GRanges object with 11399 ranges and 3 metadata columns:
##             seqnames            ranges strand |                 V5
##                <Rle>         <IRanges>  <Rle> |        <character>
##       [1]       LG11 28461480-28464481      + | ENSPREG00000010182
##       [2] KK215283.1   1375383-1378384      + | ENSPREG00000019522
##       [3] KK215283.1   1375391-1378392      - | ENSPREG00000019483
##       [4] KK215283.1   1375441-1378442      + | ENSPREG00000019522
##       [5] KK215283.1   1376555-1379556      + | ENSPREG00000019522
##       ...        ...               ...    ... .                ...
##   [11395]        LG4 11998636-12001637      + | ENSPREG00000011784
##   [11396]        LG4 11999476-12002477      + | ENSPREG00000011784
##   [11397]       LG11 23158211-23161212      - | ENSPREG00000021767
##   [11398]        LG8 23950233-23953234      - | ENSPREG00000006506
##   [11399]        LG6 25925511-25928512      - | ENSPREG00000011372
##                           V6                V7
##                  <character>       <character>
##       [1] ENSPRET00000015234            tfap2e
##       [2] ENSPRET00000029315             calua
##       [3] ENSPRET00000029113              sco2
##       [4] ENSPRET00000029364             calua
##       [5] ENSPRET00000029379             calua
##       ...                ...               ...
##   [11395] ENSPRET00000017613   uncharacterised
##   [11396] ENSPRET00000017624   uncharacterised
##   [11397] ENSPRET00000032485   uncharacterised
##   [11398] ENSPRET00000009725             CYTH3
##   [11399] ENSPRET00000017007 si:ch211-247i17.1
##   -------
##   seqinfo: 452 sequences from an unspecified genome; no seqlengths
GvLpromotersdf <- as.data.frame(GvLpromoters,row.names = 1:nrow(as.data.frame(ranges(GvLpromoters))))
str(GvLpromotersdf)
## 'data.frame':    11399 obs. of  14 variables:
##  $ seqnames   : Factor w/ 1169 levels "KK215283.1","KK215284.1",..: 1149 1 1 1 1 24 24 1165 1 1155 ...
##  $ start      : int  28461237 1376121 1376121 1376121 1376121 101373 101373 2971274 1067054 4434405 ...
##  $ end        : int  28461741 1376899 1376899 1376899 1376899 102087 102087 2971545 1067919 4435108 ...
##  $ width      : int  505 779 779 779 779 715 715 272 866 704 ...
##  $ strand     : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
##  $ L          : int  108 156 156 156 156 68 68 58 63 67 ...
##  $ area       : num  11.6 18.4 18.4 18.4 18.4 ...
##  $ beta       : num  -0.277 0.329 0.329 0.329 0.329 ...
##  $ stat       : num  -16.3 15.2 15.2 15.2 15.2 ...
##  $ pval       : num  7.14e-06 1.79e-05 1.79e-05 1.79e-05 1.79e-05 ...
##  $ qval       : num  0.654 0.749 0.749 0.749 0.749 ...
##  $ index.start: int  3678849 65611 65611 65611 65611 479142 479142 16775120 48980 8251105 ...
##  $ index.end  : int  3678956 65766 65766 65766 65766 479209 479209 16775177 49042 8251171 ...
##  $ index.width: int  108 156 156 156 156 68 68 58 63 67 ...
myPromotersoldf1 <- as.data.frame(myPromotersol1,row.names = 1:nrow(as.data.frame(ranges(myPromotersol1))))
head(myPromotersoldf1)
##     seqnames    start      end width strand                 V5
## 1       LG11 28461480 28464481  3002      + ENSPREG00000010182
## 2 KK215283.1  1375383  1378384  3002      + ENSPREG00000019522
## 3 KK215283.1  1375391  1378392  3002      - ENSPREG00000019483
## 4 KK215283.1  1375441  1378442  3002      + ENSPREG00000019522
## 5 KK215283.1  1376555  1379556  3002      + ENSPREG00000019522
## 6 KK215306.1   101374   104375  3002      - ENSPREG00000001826
##                   V6     V7
## 1 ENSPRET00000015234 tfap2e
## 2 ENSPRET00000029315  calua
## 3 ENSPRET00000029113   sco2
## 4 ENSPRET00000029364  calua
## 5 ENSPRET00000029379  calua
## 6 ENSPRET00000002537 galr1b
GvLpromotersdf <- cbind(GvLpromotersdf,myPromotersoldf1[c("V5","V6","V7")])
GvLpromotersdf$seqnames <- as.character(GvLpromotersdf$seqnames)
head(GvLpromotersdf)
##     seqnames    start      end width strand   L      area       beta      stat
## 1       LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 2 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 3 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 4 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 5 KK215283.1  1376121  1376899   779      * 156 18.407129  0.3291269  15.23454
## 6 KK215306.1   101373   102087   715      *  68  9.626653  0.4324903  12.37528
##           pval      qval index.start index.end index.width                 V5
## 1 7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010182
## 2 1.786010e-05 0.7492043       65611     65766         156 ENSPREG00000019522
## 3 1.786010e-05 0.7492043       65611     65766         156 ENSPREG00000019483
## 4 1.786010e-05 0.7492043       65611     65766         156 ENSPREG00000019522
## 5 1.786010e-05 0.7492043       65611     65766         156 ENSPREG00000019522
## 6 7.620309e-05 0.7749346      479142    479209          68 ENSPREG00000001826
##                   V6     V7
## 1 ENSPRET00000015234 tfap2e
## 2 ENSPRET00000029315  calua
## 3 ENSPRET00000029113   sco2
## 4 ENSPRET00000029364  calua
## 5 ENSPRET00000029379  calua
## 6 ENSPRET00000002537 galr1b
GvLpromoterschrdf <- GvLpromotersdf[grep("LG",GvLpromotersdf$seqnames),]
head(GvLpromoterschrdf)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 8       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10     LG17  4434405  4435108   704      *  67 10.629923 -0.4174846 -11.47364
## 11     LG17  4434405  4435108   704      *  67 10.629923 -0.4174846 -11.47364
## 12      LG4 19716877 19717452   576      *  71  4.981281  0.3020933  10.83986
## 13     LG21 16656091 16656658   568      *  92  9.790377 -0.2600441 -10.81785
##            pval      qval index.start index.end index.width                 V5
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010182
## 8  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
## 10 1.357367e-04 0.7879743     8251105   8251171          67 ENSPREG00000004307
## 11 1.357367e-04 0.7879743     8251105   8251171          67 ENSPREG00000004307
## 12 2.083678e-04 0.7879743    16318476  16318546          71 ENSPREG00000020177
## 13 2.131305e-04 0.7879743    13172129  13172220          92 ENSPREG00000015620
##                    V6              V7
## 1  ENSPRET00000015234          tfap2e
## 8  ENSPRET00000034154          asb14a
## 10 ENSPRET00000006277 uncharacterised
## 11 ENSPRET00000006277 uncharacterised
## 12 ENSPRET00000030158            ppat
## 13 ENSPRET00000023480         entpd5b
GvLpromoterschrdf <- GvLpromoterschrdf[order(GvLpromoterschrdf[,11]), ]
colnames(CvGpromoterschrdf) <- c("seqnames","start","end","width","strand","L","area", "beta","stat", "pvalue","qvalue","index.start", "index.width","L", "gene_id","transcript_id", "gene_name")
head(GvLpromoterschrdf,20)
##    seqnames    start      end width strand   L      area       beta       stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.274999
## 8       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.024079
## 10     LG17  4434405  4435108   704      *  67 10.629923 -0.4174846 -11.473637
## 11     LG17  4434405  4435108   704      *  67 10.629923 -0.4174846 -11.473637
## 12      LG4 19716877 19717452   576      *  71  4.981281  0.3020933  10.839859
## 13     LG21 16656091 16656658   568      *  92  9.790377 -0.2600441 -10.817845
## 14     LG22  8861308  8862494  1187      * 107 13.845469  0.3227734  10.238006
## 15      LG1 17897041 17897428   388      *  79  4.272873  0.2553471  10.102065
## 16     LG17  4281596  4283884  2289      * 138 14.320803  0.2363804   9.707138
## 17     LG18  4887976  4888902   927      *  70  9.621193 -0.3148876  -9.641827
## 18     LG11 12873733 12874324   592      *  65  5.977088  0.2335116   9.600946
## 19     LG19 23419961 23420381   421      *  44  2.846027 -0.2897090  -9.526620
## 20     LG13 17708262 17709123   862      *  62  9.707475  0.3562946   9.521485
## 21     LG13 17708262 17709123   862      *  62  9.707475  0.3562946   9.521485
## 22     LG18 21124909 21125756   848      *  80  6.926514  0.2445258   9.460839
## 23     LG10  5124205  5124733   529      *  91  7.418948  0.2760693   9.372552
## 24     LG10  5124205  5124733   529      *  91  7.418948  0.2760693   9.372552
## 25      LG7 27074581 27075191   611      *  76  4.468701  0.2347441   9.370081
## 26     LG17  3557984  3558729   746      *  51  9.581551  0.4594205   9.348065
## 27     LG17  3557984  3558729   746      *  51  9.581551  0.4594205   9.348065
##            pval      qval index.start index.end index.width                 V5
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010182
## 8  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
## 10 1.357367e-04 0.7879743     8251105   8251171          67 ENSPREG00000004307
## 11 1.357367e-04 0.7879743     8251105   8251171          67 ENSPREG00000004307
## 12 2.083678e-04 0.7879743    16318476  16318546          71 ENSPREG00000020177
## 13 2.131305e-04 0.7879743    13172129  13172220          92 ENSPREG00000015620
## 14 3.298165e-04 0.9737459    13711563  13711669         107 ENSPREG00000015260
## 15 3.655367e-04 0.9928849     1438366   1438444          79 ENSPREG00000004582
## 16 5.250869e-04 0.9998670     8244713   8244850         138 ENSPREG00000003984
## 17 5.536630e-04 0.9998670     9087342   9087411          70 ENSPREG00000004844
## 18 5.655698e-04 0.9998670     3222323   3222387          65 ENSPREG00000005172
## 19 6.072433e-04 0.9998670    10382933  10382976          44 ENSPREG00000020727
## 20 6.084340e-04 0.9998670     4911914   4911975          62 ENSPREG00000022956
## 21 6.084340e-04 0.9998670     4911914   4911975          62 ENSPREG00000022956
## 22 6.370102e-04 0.9998670     9609256   9609335          80 ENSPREG00000005872
## 23 6.941625e-04 0.9998670     2078042   2078132          91 ENSPREG00000022019
## 24 6.941625e-04 0.9998670     2078042   2078132          91 ENSPREG00000022019
## 25 6.965438e-04 0.9998670    19308679  19308754          76 ENSPREG00000021152
## 26 7.144039e-04 0.9998670     8216908   8216958          51 ENSPREG00000002699
## 27 7.144039e-04 0.9998670     8216908   8216958          51 ENSPREG00000002699
##                    V6              V7
## 1  ENSPRET00000015234          tfap2e
## 8  ENSPRET00000034154          asb14a
## 10 ENSPRET00000006277 uncharacterised
## 11 ENSPRET00000006277 uncharacterised
## 12 ENSPRET00000030158            ppat
## 13 ENSPRET00000023480         entpd5b
## 14 ENSPRET00000022840 uncharacterised
## 15 ENSPRET00000006703 uncharacterised
## 16 ENSPRET00000005798            MYOC
## 17 ENSPRET00000007125 uncharacterised
## 18 ENSPRET00000007618            SDC3
## 19 ENSPRET00000030962         zc3h7bb
## 20 ENSPRET00000034268 uncharacterised
## 21 ENSPRET00000034268 uncharacterised
## 22 ENSPRET00000008705 uncharacterised
## 23 ENSPRET00000032858 uncharacterised
## 24 ENSPRET00000032858 uncharacterised
## 25 ENSPRET00000031614           kmt2d
## 26 ENSPRET00000003812 uncharacterised
## 27 ENSPRET00000003834 uncharacterised
rm(GvLpromoters)
rm(GvLpromotersdf)

Create RCircos plot for CvG comparison

CvGgeneschrdfdmrs <- head(CvGgeneschrdf,75)
head(CvGgeneschrdfdmrs)
##   seqnames    start      end width strand  L      area       beta      stat
## 1     LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 3      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 5      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 6      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8     LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
##           pval      qval index.start index.end index.width            gene_id
## 1 4.013367e-05 0.7193775     4371608   4371682          75 ENSPREG00000001265
## 2 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012374
## 3 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012413
## 5 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022808
## 6 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 8 9.082882e-05 0.7193775     2481310   2481355          46 ENSPREG00000011064
##     gene_biotype gene_name
## 1 protein_coding      <NA>
## 2 protein_coding     btr30
## 3 protein_coding      <NA>
## 5 protein_coding      <NA>
## 6 protein_coding    asb14a
## 8 protein_coding     NFKB1
Chr.Label.Data <- dplyr::select(CvGgeneschrdfdmrs,seqnames,start,end,gene_name)
colnames(Chr.Label.Data) <- c("Chromosome","chromStart","chromEnd","GeneName")
head(Chr.Label.Data)
##   Chromosome chromStart chromEnd GeneName
## 1       LG13   18160946 18161700     <NA>
## 2        LG8   27368425 27368499    btr30
## 3        LG8   27368425 27368499     <NA>
## 5        LG5    2971274  2971545     <NA>
## 6        LG5    2971274  2971545   asb14a
## 8       LG10   32171882 32172301    NFKB1
Chr.Label.Data <- Chr.Label.Data[-which(Chr.Label.Data$GeneName == "" | is.na(Chr.Label.Data$GeneName)), ]
head(Chr.Label.Data,10)
##    Chromosome chromStart chromEnd GeneName
## 2         LG8   27368425 27368499    btr30
## 6         LG5    2971274  2971545   asb14a
## 8        LG10   32171882 32172301    NFKB1
## 9        LG13   18052556 18054100   capn12
## 10       LG19   10333007 10333692    QRFPR
## 11       LG19    8889655  8889899    eif3c
## 14       LG19   25883884 25884226     bbs1
## 15       LG11    3353555  3354323    kcnk9
## 18       LG10   14876068 14876399     dlg3
## 20        LG2   43981407 43981496    cry3a
head(CvGgeneschrdf)
##   seqnames    start      end width strand  L      area       beta      stat
## 1     LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 3      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 5      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 6      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8     LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
##           pval      qval index.start index.end index.width            gene_id
## 1 4.013367e-05 0.7193775     4371608   4371682          75 ENSPREG00000001265
## 2 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012374
## 3 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012413
## 5 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022808
## 6 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 8 9.082882e-05 0.7193775     2481310   2481355          46 ENSPREG00000011064
##     gene_biotype gene_name
## 1 protein_coding      <NA>
## 2 protein_coding     btr30
## 3 protein_coding      <NA>
## 5 protein_coding      <NA>
## 6 protein_coding    asb14a
## 8 protein_coding     NFKB1
RCircos.histogramV <- dplyr::select(CvGgeneschrdf,seqnames,start,end,pval)
head(RCircos.histogramV)
##   seqnames    start      end         pval
## 1     LG13 18160946 18161700 4.013367e-05
## 2      LG8 27368425 27368499 4.118982e-05
## 3      LG8 27368425 27368499 4.118982e-05
## 5      LG5  2971274  2971545 6.442510e-05
## 6      LG5  2971274  2971545 6.442510e-05
## 8     LG10 32171882 32172301 9.082882e-05
RCircos.histogramV$pval <- log(RCircos.histogramV$pval)
head(RCircos.histogramV)
##   seqnames    start      end       pval
## 1     LG13 18160946 18161700 -10.123295
## 2      LG8 27368425 27368499 -10.097320
## 3      LG8 27368425 27368499 -10.097320
## 5      LG5  2971274  2971545  -9.650007
## 6      LG5  2971274  2971545  -9.650007
## 8     LG10 32171882 32172301  -9.306534
colnames(RCircos.histogramV) <- c("Chromosome","chromStart","chromEnd","Data")
head(RCircos.histogramV)
##   Chromosome chromStart chromEnd       Data
## 1       LG13   18160946 18161700 -10.123295
## 2        LG8   27368425 27368499 -10.097320
## 3        LG8   27368425 27368499 -10.097320
## 5        LG5    2971274  2971545  -9.650007
## 6        LG5    2971274  2971545  -9.650007
## 8       LG10   32171882 32172301  -9.306534
head(CvGgeneschrdf)
##   seqnames    start      end width strand  L      area       beta      stat
## 1     LG13 18160946 18161700   755      * 75 17.104340  0.4804793  12.35578
## 2      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 3      LG8 27368425 27368499    75      * 22  1.107603 -0.3598625 -12.34614
## 5      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 6      LG5  2971274  2971545   272      * 61  8.495669  0.3785743  11.65333
## 8     LG10 32171882 32172301   420      * 46  8.597024  0.4390605  11.17294
##           pval      qval index.start index.end index.width            gene_id
## 1 4.013367e-05 0.7193775     4371608   4371682          75 ENSPREG00000001265
## 2 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012374
## 3 4.118982e-05 0.7193775    18010981  18011002          22 ENSPREG00000012413
## 5 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022808
## 6 6.442510e-05 0.7193775    14903599  14903659          61 ENSPREG00000022867
## 8 9.082882e-05 0.7193775     2481310   2481355          46 ENSPREG00000011064
##     gene_biotype gene_name
## 1 protein_coding      <NA>
## 2 protein_coding     btr30
## 3 protein_coding      <NA>
## 5 protein_coding      <NA>
## 6 protein_coding    asb14a
## 8 protein_coding     NFKB1
RCircos.heatmapV <- dplyr::select(CvGgeneschrdf,seqnames,start,end,gene_name,beta)
head(RCircos.heatmapV)
##   seqnames    start      end gene_name       beta
## 1     LG13 18160946 18161700      <NA>  0.4804793
## 2      LG8 27368425 27368499     btr30 -0.3598625
## 3      LG8 27368425 27368499      <NA> -0.3598625
## 5      LG5  2971274  2971545      <NA>  0.3785743
## 6      LG5  2971274  2971545    asb14a  0.3785743
## 8     LG10 32171882 32172301     NFKB1  0.4390605
colnames(RCircos.heatmapV) <- c("Chromosome","chromStart","chromEnd","GeneName","CvG")
head(RCircos.heatmapV)
##   Chromosome chromStart chromEnd GeneName        CvG
## 1       LG13   18160946 18161700     <NA>  0.4804793
## 2        LG8   27368425 27368499    btr30 -0.3598625
## 3        LG8   27368425 27368499     <NA> -0.3598625
## 5        LG5    2971274  2971545     <NA>  0.3785743
## 6        LG5    2971274  2971545   asb14a  0.3785743
## 8       LG10   32171882 32172301    NFKB1  0.4390605
data(UCSC.Mouse.GRCm38.CytoBandIdeogram)
str(UCSC.Mouse.GRCm38.CytoBandIdeogram)
## 'data.frame':    403 obs. of  5 variables:
##  $ Chromosome: Factor w/ 21 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ ChromStart: int  0 8840440 12278390 20136559 22101102 30941543 43219933 54516052 55989459 59427408 ...
##  $ ChromEnd  : int  8840440 12278390 20136559 22101102 30941543 43219933 54516052 55989459 59427408 65321035 ...
##  $ Band      : Factor w/ 97 levels "qA","qA1","qA1.1",..: 2 6 7 11 12 20 40 41 42 43 ...
##  $ Stain     : Factor w/ 5 levels "gneg","gpos100",..: 2 1 3 1 2 1 4 1 5 1 ...
chrlen <- read.table("/mnt/data/aaron/projects/guppy-methylation/chrlen.tsv")
str(chrlen)
## 'data.frame':    23 obs. of  2 variables:
##  $ V1: chr  "LG1" "LG2" "LG3" "LG4" ...
##  $ V2: int  34115677 46286544 35265442 31497199 33908744 31529174 31413364 27946405 34117797 32819797 ...
segs <- apply(X = chrlen,MARGIN = 1,FUN = function(l){
chr <- l[1]
len <- l[2]
seg <- seq(1,len,1000000)
df <- data.frame(chr,as.integer(seg),as.integer(seg+999999))
df$band <- paste("x",1:nrow(df),sep = "")
stain <- c("gneg","gpos")
df$stain <- as.vector(matrix(data = stain,nrow = nrow(df),ncol = 1))
return(df)
})
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [35]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [47]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [35]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [33]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [29]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [27]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [29]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [31]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [31]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [23]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [29]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [27]
## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded

## Warning in data.frame(chr, as.integer(seg), as.integer(seg + 999999)): row names
## were found from a short variable and have been discarded
## Warning in matrix(data = stain, nrow = nrow(df), ncol = 1): data length [2] is
## not a sub-multiple or multiple of the number of rows [19]
segs <- do.call(rbind, segs)
colnames(segs) <- c("Chromosome","ChromStart","ChromEnd","Band","Stain")
str(segs)
## 'data.frame':    709 obs. of  5 variables:
##  $ Chromosome: chr  "LG1" "LG1" "LG1" "LG1" ...
##  $ ChromStart: int  1 1000001 2000001 3000001 4000001 5000001 6000001 7000001 8000001 9000001 ...
##  $ ChromEnd  : int  1000000 2000000 3000000 4000000 5000000 6000000 7000000 8000000 9000000 10000000 ...
##  $ Band      : chr  "x1" "x2" "x3" "x4" ...
##  $ Stain     : chr  "gneg" "gpos" "gneg" "gpos" ...
head(segs)
##   Chromosome ChromStart ChromEnd Band Stain
## 1        LG1          1  1000000   x1  gneg
## 2        LG1    1000001  2000000   x2  gpos
## 3        LG1    2000001  3000000   x3  gneg
## 4        LG1    3000001  4000000   x4  gpos
## 5        LG1    4000001  5000000   x5  gneg
## 6        LG1    5000001  6000000   x6  gpos
RCircos.Set.Core.Components(cyto.info = segs,tracks.inside = 4,chr.exclude = NULL,tracks.outside = 0)
## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.
rcircos.params <- RCircos.Get.Plot.Parameters()
rcircos.cyto <- RCircos.Get.Plot.Ideogram()
rcircos.position <- RCircos.Get.Plot.Positions()
rcircos.params$hist.width <- 30
rcircos.params$heatmap.width <- 30
rcircos.params$text.size <- 0.75
RCircos.Reset.Plot.Parameters(new.params = rcircos.params)
#out.file <- "RCircosGuppyMethylome.pdf";
#pdf(file=out.file, height=8, width=8, compress=TRUE)
#Setup RCircos plot
plot.new()
RCircos.Set.Plot.Area()
#Include ideogram
RCircos.Chromosome.Ideogram.Plot()
data(RCircos.histogramV)
## Warning in data(RCircos.histogramV): data set 'RCircos.histogramV' not found
#Create Heatmap
data(RCircos.heatmapV)
## Warning in data(RCircos.heatmapV): data set 'RCircos.heatmapV' not found
RCircos.Heatmap.Plot(heatmap.data = head(RCircos.heatmapV,75), data.col = 5,track.num = 1,side = "in")
#Create histogram
RCircos.Histogram.Plot(head(RCircos.histogramV,75),data.col=4, track.num=2, side="in")
#Include gene names and create connectors to histogram
RCircos.Gene.Connector.Plot(genomic.data = Chr.Label.Data,track.num = 3, side = "in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.
RCircos.Gene.Name.Plot(head(Chr.Label.Data,75), name.col=4,track.num=4, side="in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.

Create RCircos plot for CvL comparison

CvLgeneschrdfdmrs <- head(CvLgeneschrdf,75)
head(CvLgeneschrdfdmrs)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 3      LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6       LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 7      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
## 8      LG14  4297874  4299069  1196      * 45  9.873079 -0.4990115 -10.64895
## 10     LG12 21371716 21372025   310      * 58  3.735525 -0.3274811 -10.48784
##            pval      qval index.start index.end index.width            gene_id
## 1  9.999990e-07 0.1114369     8673138   8673208          71 ENSPREG00000002350
## 3  6.599993e-05 0.9103295     4374338   4374419          82 ENSPREG00000006590
## 6  7.399993e-05 0.9103295    17405986  17406045          60 ENSPREG00000011882
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  1.209999e-04 0.9103295     4766186   4766230          45 ENSPREG00000009813
## 10 1.389999e-04 0.9103295     3729020   3729077          58 ENSPREG00000019970
##      gene_biotype gene_name
## 1  protein_coding     QRFPR
## 3  protein_coding  ankrd13b
## 6  protein_coding  rapgefl1
## 7  protein_coding      <NA>
## 8  protein_coding    rab34b
## 10 protein_coding      <NA>
Chr.Label.Data <- dplyr::select(CvLgeneschrdfdmrs,seqnames,start,end,gene_name)
colnames(Chr.Label.Data) <- c("Chromosome","chromStart","chromEnd","GeneName")
head(Chr.Label.Data)
##    Chromosome chromStart chromEnd GeneName
## 1        LG19   10333007 10333692    QRFPR
## 3        LG13   22015858 22016352 ankrd13b
## 6         LG8   18982718 18983377 rapgefl1
## 7        LG11   14181818 14182182     <NA>
## 8        LG14    4297874  4299069   rab34b
## 10       LG12   21371716 21372025     <NA>
Chr.Label.Data <- Chr.Label.Data[-which(Chr.Label.Data$GeneName == "" | is.na(Chr.Label.Data$GeneName)), ]
head(Chr.Label.Data, 10)
##    Chromosome chromStart chromEnd GeneName
## 1        LG19   10333007 10333692    QRFPR
## 3        LG13   22015858 22016352 ankrd13b
## 6         LG8   18982718 18983377 rapgefl1
## 8        LG14    4297874  4299069   rab34b
## 11       LG19    1188386  1188923   SHANK1
## 12       LG19   28150293 28151137  bhlha15
## 13       LG16     483733   484086   atp2c1
## 14       LG22    9760595  9760997   map4k5
## 15        LG1   31411882 31412386     bnc2
## 17        LG1    5775276  5777164  fam20cl
head(CvLgeneschrdf)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 3      LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6       LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 7      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
## 8      LG14  4297874  4299069  1196      * 45  9.873079 -0.4990115 -10.64895
## 10     LG12 21371716 21372025   310      * 58  3.735525 -0.3274811 -10.48784
##            pval      qval index.start index.end index.width            gene_id
## 1  9.999990e-07 0.1114369     8673138   8673208          71 ENSPREG00000002350
## 3  6.599993e-05 0.9103295     4374338   4374419          82 ENSPREG00000006590
## 6  7.399993e-05 0.9103295    17405986  17406045          60 ENSPREG00000011882
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  1.209999e-04 0.9103295     4766186   4766230          45 ENSPREG00000009813
## 10 1.389999e-04 0.9103295     3729020   3729077          58 ENSPREG00000019970
##      gene_biotype gene_name
## 1  protein_coding     QRFPR
## 3  protein_coding  ankrd13b
## 6  protein_coding  rapgefl1
## 7  protein_coding      <NA>
## 8  protein_coding    rab34b
## 10 protein_coding      <NA>
RCircos.histogramV <- dplyr::select(CvLgeneschrdf,seqnames,start,end,pval)
head(RCircos.histogramV)
##    seqnames    start      end         pval
## 1      LG19 10333007 10333692 9.999990e-07
## 3      LG13 22015858 22016352 6.599993e-05
## 6       LG8 18982718 18983377 7.399993e-05
## 7      LG11 14181818 14182182 8.099992e-05
## 8      LG14  4297874  4299069 1.209999e-04
## 10     LG12 21371716 21372025 1.389999e-04
RCircos.histogramV$pval <- log(RCircos.histogramV$pval)
head(RCircos.histogramV)
##    seqnames    start      end       pval
## 1      LG19 10333007 10333692 -13.815512
## 3      LG13 22015858 22016352  -9.625857
## 6       LG8 18982718 18983377  -9.511446
## 7      LG11 14181818 14182182  -9.421062
## 8      LG14  4297874  4299069  -9.019721
## 10     LG12 21371716 21372025  -8.881038
colnames(RCircos.histogramV) <- c("Chromosome","chromStart","chromEnd","Data")
head(RCircos.histogramV)
##    Chromosome chromStart chromEnd       Data
## 1        LG19   10333007 10333692 -13.815512
## 3        LG13   22015858 22016352  -9.625857
## 6         LG8   18982718 18983377  -9.511446
## 7        LG11   14181818 14182182  -9.421062
## 8        LG14    4297874  4299069  -9.019721
## 10       LG12   21371716 21372025  -8.881038
head(CvLgeneschrdf)
##    seqnames    start      end width strand  L      area       beta      stat
## 1      LG19 10333007 10333692   686      * 71 16.559670  0.5767663  18.99209
## 3      LG13 22015858 22016352   495      * 82 14.226193  0.4397952  11.57442
## 6       LG8 18982718 18983377   660      * 60  7.212046 -0.3746378 -11.38354
## 7      LG11 14181818 14182182   365      * 58  4.745863 -0.3570840 -11.25378
## 8      LG14  4297874  4299069  1196      * 45  9.873079 -0.4990115 -10.64895
## 10     LG12 21371716 21372025   310      * 58  3.735525 -0.3274811 -10.48784
##            pval      qval index.start index.end index.width            gene_id
## 1  9.999990e-07 0.1114369     8673138   8673208          71 ENSPREG00000002350
## 3  6.599993e-05 0.9103295     4374338   4374419          82 ENSPREG00000006590
## 6  7.399993e-05 0.9103295    17405986  17406045          60 ENSPREG00000011882
## 7  8.099992e-05 0.9103295     2836015   2836072          58 ENSPREG00000007449
## 8  1.209999e-04 0.9103295     4766186   4766230          45 ENSPREG00000009813
## 10 1.389999e-04 0.9103295     3729020   3729077          58 ENSPREG00000019970
##      gene_biotype gene_name
## 1  protein_coding     QRFPR
## 3  protein_coding  ankrd13b
## 6  protein_coding  rapgefl1
## 7  protein_coding      <NA>
## 8  protein_coding    rab34b
## 10 protein_coding      <NA>
RCircos.heatmapV <- dplyr::select(CvLgeneschrdf,seqnames,start,end,gene_name,beta)
head(RCircos.heatmapV)
##    seqnames    start      end gene_name       beta
## 1      LG19 10333007 10333692     QRFPR  0.5767663
## 3      LG13 22015858 22016352  ankrd13b  0.4397952
## 6       LG8 18982718 18983377  rapgefl1 -0.3746378
## 7      LG11 14181818 14182182      <NA> -0.3570840
## 8      LG14  4297874  4299069    rab34b -0.4990115
## 10     LG12 21371716 21372025      <NA> -0.3274811
colnames(RCircos.heatmapV) <- c("Chromosome","chromStart","chromEnd","GeneName","CvG")
head(RCircos.heatmapV)
##    Chromosome chromStart chromEnd GeneName        CvG
## 1        LG19   10333007 10333692    QRFPR  0.5767663
## 3        LG13   22015858 22016352 ankrd13b  0.4397952
## 6         LG8   18982718 18983377 rapgefl1 -0.3746378
## 7        LG11   14181818 14182182     <NA> -0.3570840
## 8        LG14    4297874  4299069   rab34b -0.4990115
## 10       LG12   21371716 21372025     <NA> -0.3274811
RCircos.Set.Core.Components(cyto.info = segs,tracks.inside = 4,chr.exclude = NULL,tracks.outside = 0)
## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.
rcircos.params <- RCircos.Get.Plot.Parameters()
rcircos.cyto <- RCircos.Get.Plot.Ideogram()
rcircos.position <- RCircos.Get.Plot.Positions()
rcircos.params$hist.width <- 30
rcircos.params$heatmap.width <- 30
rcircos.params$text.size <- 0.75
RCircos.Reset.Plot.Parameters(new.params = rcircos.params)
#out.file <- "RCircosGuppyMethylome.pdf";
#pdf(file=out.file, height=8, width=8, compress=TRUE)
#Setup RCircos plot
plot.new()
RCircos.Set.Plot.Area()
#Include ideogram
RCircos.Chromosome.Ideogram.Plot()
data(RCircos.histogramV)
## Warning in data(RCircos.histogramV): data set 'RCircos.histogramV' not found
#Create Heatmap
data(RCircos.heatmapV)
## Warning in data(RCircos.heatmapV): data set 'RCircos.heatmapV' not found
RCircos.Heatmap.Plot(heatmap.data = head(RCircos.heatmapV,75), data.col = 5,track.num = 1,side = "in")
#Create histogram
RCircos.Histogram.Plot(head(RCircos.histogramV,75),data.col=4, track.num=2, side="in")
#Include gene names and create connectors to histogram
RCircos.Gene.Connector.Plot(genomic.data = Chr.Label.Data,track.num = 3, side = "in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.
RCircos.Gene.Name.Plot(head(Chr.Label.Data,75), name.col=4,track.num=4, side="in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.

Create RCircos plot for GvL comparison

CvLgeneschrdfdmrs <- head(GvLgeneschrdf,75)
head(CvLgeneschrdfdmrs)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 4       LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 5      LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7      LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10      LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##            pval      qval index.start index.end index.width            gene_id
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010167
## 4  5.477097e-05 0.7492043    11413014  11413078          65 ENSPREG00000001027
## 5  5.596164e-05 0.7492043     4929871   4929965          95 ENSPREG00000001265
## 7  6.548703e-05 0.7492043     3123427   3123501          75 ENSPREG00000021580
## 9  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022808
## 10 9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
##      gene_biotype gene_name
## 1  protein_coding      ncdn
## 4  protein_coding     casq2
## 5  protein_coding      <NA>
## 7  protein_coding    jazf1a
## 9  protein_coding      <NA>
## 10 protein_coding    asb14a
Chr.Label.Data <- dplyr::select(CvLgeneschrdfdmrs,seqnames,start,end,gene_name)
colnames(Chr.Label.Data) <- c("Chromosome","chromStart","chromEnd","GeneName")
head(Chr.Label.Data)
##    Chromosome chromStart chromEnd GeneName
## 1        LG11   28461237 28461741     ncdn
## 4         LG2   28494008 28495445    casq2
## 5        LG13   18160946 18161831     <NA>
## 7        LG11   10041760 10042135   jazf1a
## 9         LG5    2971274  2971545     <NA>
## 10        LG5    2971274  2971545   asb14a
Chr.Label.Data <- Chr.Label.Data[-which(Chr.Label.Data$GeneName == "" | is.na(Chr.Label.Data$GeneName)), ]
head(Chr.Label.Data,10)
##    Chromosome chromStart chromEnd GeneName
## 1        LG11   28461237 28461741     ncdn
## 4         LG2   28494008 28495445    casq2
## 7        LG11   10041760 10042135   jazf1a
## 10        LG5    2971274  2971545   asb14a
## 15        LG5   19662076 19662488  dlgap4b
## 16        LG3   31400775 31402677  shank2a
## 17        LG2   45915064 45915398    mstnb
## 18        LG3    9883425  9885124     scg3
## 19        LG4   19716877 19717452     ppat
## 20        LG4   19716877 19717452    paics
head(GvLgeneschrdf)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 4       LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 5      LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7      LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10      LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##            pval      qval index.start index.end index.width            gene_id
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010167
## 4  5.477097e-05 0.7492043    11413014  11413078          65 ENSPREG00000001027
## 5  5.596164e-05 0.7492043     4929871   4929965          95 ENSPREG00000001265
## 7  6.548703e-05 0.7492043     3123427   3123501          75 ENSPREG00000021580
## 9  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022808
## 10 9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
##      gene_biotype gene_name
## 1  protein_coding      ncdn
## 4  protein_coding     casq2
## 5  protein_coding      <NA>
## 7  protein_coding    jazf1a
## 9  protein_coding      <NA>
## 10 protein_coding    asb14a
RCircos.histogramV <- dplyr::select(GvLgeneschrdf,seqnames,start,end,pval)
head(RCircos.histogramV)
##    seqnames    start      end         pval
## 1      LG11 28461237 28461741 7.144039e-06
## 4       LG2 28494008 28495445 5.477097e-05
## 5      LG13 18160946 18161831 5.596164e-05
## 7      LG11 10041760 10042135 6.548703e-05
## 9       LG5  2971274  2971545 9.287251e-05
## 10      LG5  2971274  2971545 9.287251e-05
RCircos.histogramV$pval <- log(RCircos.histogramV$pval)
head(RCircos.histogramV)
##    seqnames    start      end       pval
## 1      LG11 28461237 28461741 -11.849232
## 4       LG2 28494008 28495445  -9.812350
## 5      LG13 18160946 18161831  -9.790844
## 7      LG11 10041760 10042135  -9.633658
## 9       LG5  2971274  2971545  -9.284283
## 10      LG5  2971274  2971545  -9.284283
colnames(RCircos.histogramV) <- c("Chromosome","chromStart","chromEnd","Data")
head(RCircos.histogramV)
##    Chromosome chromStart chromEnd       Data
## 1        LG11   28461237 28461741 -11.849232
## 4         LG2   28494008 28495445  -9.812350
## 5        LG13   18160946 18161831  -9.790844
## 7        LG11   10041760 10042135  -9.633658
## 9         LG5    2971274  2971545  -9.284283
## 10        LG5    2971274  2971545  -9.284283
head(GvLgeneschrdf)
##    seqnames    start      end width strand   L      area       beta      stat
## 1      LG11 28461237 28461741   505      * 108 11.636971 -0.2773737 -16.27500
## 4       LG2 28494008 28495445  1438      *  65  9.709663  0.4626823  12.85427
## 5      LG13 18160946 18161831   886      *  95 16.311864 -0.3970642 -12.75740
## 7      LG11 10041760 10042135   376      *  75  6.666626  0.3701602  12.64751
## 9       LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
## 10      LG5  2971274  2971545   272      *  58  7.527239 -0.3990748 -12.02408
##            pval      qval index.start index.end index.width            gene_id
## 1  7.144039e-06 0.6538511     3678849   3678956         108 ENSPREG00000010167
## 4  5.477097e-05 0.7492043    11413014  11413078          65 ENSPREG00000001027
## 5  5.596164e-05 0.7492043     4929871   4929965          95 ENSPREG00000001265
## 7  6.548703e-05 0.7492043     3123427   3123501          75 ENSPREG00000021580
## 9  9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022808
## 10 9.287251e-05 0.7879743    16775120  16775177          58 ENSPREG00000022867
##      gene_biotype gene_name
## 1  protein_coding      ncdn
## 4  protein_coding     casq2
## 5  protein_coding      <NA>
## 7  protein_coding    jazf1a
## 9  protein_coding      <NA>
## 10 protein_coding    asb14a
RCircos.heatmapV <- dplyr::select(GvLgeneschrdf,seqnames,start,end,gene_name,beta)
head(RCircos.heatmapV)
##    seqnames    start      end gene_name       beta
## 1      LG11 28461237 28461741      ncdn -0.2773737
## 4       LG2 28494008 28495445     casq2  0.4626823
## 5      LG13 18160946 18161831      <NA> -0.3970642
## 7      LG11 10041760 10042135    jazf1a  0.3701602
## 9       LG5  2971274  2971545      <NA> -0.3990748
## 10      LG5  2971274  2971545    asb14a -0.3990748
colnames(RCircos.heatmapV) <- c("Chromosome","chromStart","chromEnd","GeneName","CvG")
head(RCircos.heatmapV)
##    Chromosome chromStart chromEnd GeneName        CvG
## 1        LG11   28461237 28461741     ncdn -0.2773737
## 4         LG2   28494008 28495445    casq2  0.4626823
## 5        LG13   18160946 18161831     <NA> -0.3970642
## 7        LG11   10041760 10042135   jazf1a  0.3701602
## 9         LG5    2971274  2971545     <NA> -0.3990748
## 10        LG5    2971274  2971545   asb14a -0.3990748
RCircos.Set.Core.Components(cyto.info = segs,tracks.inside = 4,chr.exclude = NULL,tracks.outside = 0)
## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.
rcircos.params <- RCircos.Get.Plot.Parameters()
rcircos.cyto <- RCircos.Get.Plot.Ideogram()
rcircos.position <- RCircos.Get.Plot.Positions()
rcircos.params$hist.width <- 30
rcircos.params$heatmap.width <- 30
rcircos.params$text.size <- 0.75
RCircos.Reset.Plot.Parameters(new.params = rcircos.params)
#out.file <- "RCircosGuppyMethylome.pdf";
#pdf(file=out.file, height=8, width=8, compress=TRUE)
#Setup RCircos plot
plot.new()
RCircos.Set.Plot.Area()
#Include ideogram
RCircos.Chromosome.Ideogram.Plot()
data(RCircos.histogramV)
## Warning in data(RCircos.histogramV): data set 'RCircos.histogramV' not found
#Create Heatmap
data(RCircos.heatmapV)
## Warning in data(RCircos.heatmapV): data set 'RCircos.heatmapV' not found
RCircos.Heatmap.Plot(heatmap.data = head(RCircos.heatmapV,75), data.col = 5,track.num = 1,side = "in")
#Create histogram
RCircos.Histogram.Plot(head(RCircos.histogramV,75),data.col=4, track.num=2, side="in")
#Include gene names and create connectors to histogram
RCircos.Gene.Connector.Plot(genomic.data = Chr.Label.Data,track.num = 3, side = "in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.
RCircos.Gene.Name.Plot(head(Chr.Label.Data,75), name.col=4,track.num=4, side="in")
## There is unsupported chromosome names in ideogram
## and chromosomes are sorted in alphabetical order.
## Not all labels will be plotted.
## Type RCircos.Get.Gene.Name.Plot.Parameters()
## to see the number of labels for each chromosome.

Read in the methylation data from Biscuit

ClearR1 <- read.table("meth_data/Clear2F-R1.bam.vcf.gz.cg.bed.gz")
ClearR2 <- read.table("meth_data/Clear2F-R2.bam.vcf.gz.cg.bed.gz")
ClearR3 <- read.table("meth_data/Clear2F-R3.bam.vcf.gz.cg.bed.gz")
Foundation <- read.table("meth_data/Foundation.bam.vcf.gz.cg.bed.gz")
GreenR1 <- read.table("meth_data/Green3F-R1.bam.vcf.gz.cg.bed.gz")
GreenR2 <- read.table("meth_data/Green3F-R2.bam.vcf.gz.cg.bed.gz")
GreenR3 <- read.table("meth_data/Green3F-R3.bam.vcf.gz.cg.bed.gz")
LilacR1 <- read.table("meth_data/Lilac4F-R1.bam.vcf.gz.cg.bed.gz")
LilacR2 <- read.table("meth_data/Lilac4F-R2.bam.vcf.gz.cg.bed.gz")
LilacR3 <- read.table("meth_data/Lilac4F-R3.bam.vcf.gz.cg.bed.gz")

Make some plots to investigate CpG methylation in DMRs

library(vioplot)
## Loading required package: sm
## Package 'sm', version 2.2-5.7: type help(sm) for summary information
## Loading required package: zoo
## 
## Attaching package: 'zoo'
## The following objects are masked from 'package:base':
## 
##     as.Date, as.Date.numeric
library(beeswarm)

dmrplots <- function(dmr){

  dmrseqname <- dmr[1]
  dmrstart <- dmr[2]
  dmrend <- dmr[3]
  gene_name <- dmr[17]
  
  Foundationsub <- Foundation[which( Foundation$V1==dmrseqname & Foundation$V2>dmrstart & Foundation$V3<dmrend ),4]
  ClearR1sub <- ClearR1[which( ClearR1$V1==dmrseqname & ClearR1$V2>dmrstart & ClearR1$V3<dmrend ),4]
  ClearR2sub <- ClearR2[which( ClearR2$V1==dmrseqname & ClearR2$V2>dmrstart & ClearR2$V3<dmrend ),4]
  ClearR3sub <- ClearR3[which( ClearR3$V1==dmrseqname & ClearR3$V2>dmrstart & ClearR3$V3<dmrend ),4]
  GreenR1sub <- GreenR1[which( GreenR1$V1==dmrseqname & GreenR1$V2>dmrstart & GreenR1$V3<dmrend ),4]
  GreenR2sub <- GreenR2[which( GreenR2$V1==dmrseqname & GreenR2$V2>dmrstart & GreenR2$V3<dmrend ),4]
  GreenR3sub <- GreenR3[which( GreenR3$V1==dmrseqname & GreenR3$V2>dmrstart & GreenR3$V3<dmrend ),4]
  LilacR1sub <- LilacR1[which( LilacR1$V1==dmrseqname & LilacR1$V2>dmrstart & LilacR1$V3<dmrend ),4]
  LilacR2sub <- LilacR2[which( LilacR2$V1==dmrseqname & LilacR2$V2>dmrstart & LilacR2$V3<dmrend ),4]
  LilacR3sub <- LilacR3[which( LilacR3$V1==dmrseqname & LilacR3$V2>dmrstart & LilacR3$V3<dmrend ),4]
  
  ml <- list("Foundation"=Foundationsub,
             "ClearR1"=ClearR1sub,
             "ClearR2"=ClearR2sub,
             "ClearR3"=ClearR3sub,
             "GreenR1"=GreenR1sub,
             "GreenR2"=GreenR2sub,
             "GreenR3"=GreenR3sub,
             "LilacR1"=LilacR1sub,
             "LilacR2"=LilacR2sub,
             "LilacR3"=LilacR3sub)
  HEADER = paste(dmrseqname,dmrstart,dmrend,gene_name)
  par(mar=c(5,10,3,1))
  vioplot(ml, main = HEADER, xlab = "% Methylation",  horizontal=TRUE,las=1)
  beeswarm(ml, main = HEADER,  xlab = "% Methylation", horizontal = TRUE, las=1,pch=19,cex=0.5)
  mlm <- unlist(lapply(ml,mean))
  barplot( mlm, main = HEADER, xlab = "% Methylation", horiz=TRUE,las=1,xlim=c(min(mlm)-0.01,max(mlm)+0.01))
}

# test that one works
# dmr <- CvGgeneschrdf[1,,drop=TRUE]
# dmrplots(dmr)

# with lapply
lapply(X=1:10, function(i) {
  dmr <- CvGgeneschrdf[i,,drop=TRUE]
  dmrplots(dmr)
})

## [[1]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[2]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[3]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[4]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[5]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[6]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[7]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[8]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[9]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[10]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
library(vioplot)
library(beeswarm)

dmrplots <- function(dmr){

  dmrseqname <- dmr[1]
  dmrstart <- dmr[2]
  dmrend <- dmr[3]
  gene_name <- dmr[17]
  
  Foundationsub <- Foundation[which( Foundation$V1==dmrseqname & Foundation$V2>dmrstart & Foundation$V3<dmrend ),4]
  ClearR1sub <- ClearR1[which( ClearR1$V1==dmrseqname & ClearR1$V2>dmrstart & ClearR1$V3<dmrend ),4]
  ClearR2sub <- ClearR2[which( ClearR2$V1==dmrseqname & ClearR2$V2>dmrstart & ClearR2$V3<dmrend ),4]
  ClearR3sub <- ClearR3[which( ClearR3$V1==dmrseqname & ClearR3$V2>dmrstart & ClearR3$V3<dmrend ),4]
  GreenR1sub <- GreenR1[which( GreenR1$V1==dmrseqname & GreenR1$V2>dmrstart & GreenR1$V3<dmrend ),4]
  GreenR2sub <- GreenR2[which( GreenR2$V1==dmrseqname & GreenR2$V2>dmrstart & GreenR2$V3<dmrend ),4]
  GreenR3sub <- GreenR3[which( GreenR3$V1==dmrseqname & GreenR3$V2>dmrstart & GreenR3$V3<dmrend ),4]
  LilacR1sub <- LilacR1[which( LilacR1$V1==dmrseqname & LilacR1$V2>dmrstart & LilacR1$V3<dmrend ),4]
  LilacR2sub <- LilacR2[which( LilacR2$V1==dmrseqname & LilacR2$V2>dmrstart & LilacR2$V3<dmrend ),4]
  LilacR3sub <- LilacR3[which( LilacR3$V1==dmrseqname & LilacR3$V2>dmrstart & LilacR3$V3<dmrend ),4]
  
  ml <- list("Foundation"=Foundationsub,
             "ClearR1"=ClearR1sub,
             "ClearR2"=ClearR2sub,
             "ClearR3"=ClearR3sub,
             "GreenR1"=GreenR1sub,
             "GreenR2"=GreenR2sub,
             "GreenR3"=GreenR3sub,
             "LilacR1"=LilacR1sub,
             "LilacR2"=LilacR2sub,
             "LilacR3"=LilacR3sub)
  HEADER = paste(dmrseqname,dmrstart,dmrend,gene_name)
  par(mar=c(5,10,3,1))
  vioplot(ml, main = HEADER, xlab = "% Methylation",  horizontal=TRUE,las=1)
  beeswarm(ml, main = HEADER,  xlab = "% Methylation", horizontal = TRUE, las=1,pch=19,cex=0.5)
  mlm <- unlist(lapply(ml,mean))
  barplot( mlm, main = HEADER, xlab = "% Methylation", horiz=TRUE,las=1,xlim=c(min(mlm)-0.01,max(mlm)+0.01))
}

# test that one works
# dmr <- CvLgeneschrdf[1,,drop=TRUE]
# dmrplots(dmr)

# with lapply
lapply(X=1:10, function(i) {
  dmr <- CvLgeneschrdf[i,,drop=TRUE]
  dmrplots(dmr)
})

## [[1]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[2]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[3]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[4]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[5]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[6]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[7]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[8]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[9]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[10]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
library(vioplot)
library(beeswarm)

dmrplots <- function(dmr){

  dmrseqname <- dmr[1]
  dmrstart <- dmr[2]
  dmrend <- dmr[3]
  gene_name <- dmr[17]
  
  Foundationsub <- Foundation[which( Foundation$V1==dmrseqname & Foundation$V2>dmrstart & Foundation$V3<dmrend ),4]
  ClearR1sub <- ClearR1[which( ClearR1$V1==dmrseqname & ClearR1$V2>dmrstart & ClearR1$V3<dmrend ),4]
  ClearR2sub <- ClearR2[which( ClearR2$V1==dmrseqname & ClearR2$V2>dmrstart & ClearR2$V3<dmrend ),4]
  ClearR3sub <- ClearR3[which( ClearR3$V1==dmrseqname & ClearR3$V2>dmrstart & ClearR3$V3<dmrend ),4]
  GreenR1sub <- GreenR1[which( GreenR1$V1==dmrseqname & GreenR1$V2>dmrstart & GreenR1$V3<dmrend ),4]
  GreenR2sub <- GreenR2[which( GreenR2$V1==dmrseqname & GreenR2$V2>dmrstart & GreenR2$V3<dmrend ),4]
  GreenR3sub <- GreenR3[which( GreenR3$V1==dmrseqname & GreenR3$V2>dmrstart & GreenR3$V3<dmrend ),4]
  LilacR1sub <- LilacR1[which( LilacR1$V1==dmrseqname & LilacR1$V2>dmrstart & LilacR1$V3<dmrend ),4]
  LilacR2sub <- LilacR2[which( LilacR2$V1==dmrseqname & LilacR2$V2>dmrstart & LilacR2$V3<dmrend ),4]
  LilacR3sub <- LilacR3[which( LilacR3$V1==dmrseqname & LilacR3$V2>dmrstart & LilacR3$V3<dmrend ),4]
  
  ml <- list("Foundation"=Foundationsub,
             "ClearR1"=ClearR1sub,
             "ClearR2"=ClearR2sub,
             "ClearR3"=ClearR3sub,
             "GreenR1"=GreenR1sub,
             "GreenR2"=GreenR2sub,
             "GreenR3"=GreenR3sub,
             "LilacR1"=LilacR1sub,
             "LilacR2"=LilacR2sub,
             "LilacR3"=LilacR3sub)
  HEADER = paste(dmrseqname,dmrstart,dmrend,gene_name)
  par(mar=c(5,10,3,1))
  vioplot(ml, main = HEADER, xlab = "% Methylation",  horizontal=TRUE,las=1)
  beeswarm(ml, main = HEADER,  xlab = "% Methylation", horizontal = TRUE, las=1,pch=19,cex=0.5)
  mlm <- unlist(lapply(ml,mean))
  barplot( mlm, main = HEADER, xlab = "% Methylation", horiz=TRUE,las=1,xlim=c(min(mlm)-0.01,max(mlm)+0.01))
}

# test that one works
# dmr <- GvLgeneschrdf[1,,drop=TRUE]
# dmrplots(dmr)

# with lapply
lapply(X=1:10, function(i) {
  dmr <- GvLgeneschrdf[i,,drop=TRUE]
  dmrplots(dmr)
})

## [[1]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[2]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[3]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[4]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[5]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[6]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[7]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[8]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[9]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5
## 
## [[10]]
##       [,1]
##  [1,]  0.7
##  [2,]  1.9
##  [3,]  3.1
##  [4,]  4.3
##  [5,]  5.5
##  [6,]  6.7
##  [7,]  7.9
##  [8,]  9.1
##  [9,] 10.3
## [10,] 11.5

Session Information

For reproducibility

sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
##  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
##  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] beeswarm_0.4.0         vioplot_0.3.7          zoo_1.8-9             
##  [4] sm_2.2-5.7             data.table_1.14.0      dplyr_1.0.7           
##  [7] RCircos_1.2.1          BiocManager_1.30.16    GenomicFeatures_1.44.2
## [10] AnnotationDbi_1.54.1   Biobase_2.52.0         GenomicRanges_1.44.0  
## [13] GenomeInfoDb_1.28.4    IRanges_2.26.0         S4Vectors_0.30.0      
## [16] BiocGenerics_0.38.0   
## 
## loaded via a namespace (and not attached):
##  [1] MatrixGenerics_1.4.3        httr_1.4.2                 
##  [3] sass_0.4.0                  bit64_4.0.5                
##  [5] jsonlite_1.7.2              bslib_0.3.0                
##  [7] assertthat_0.2.1            highr_0.9                  
##  [9] BiocFileCache_2.0.0         blob_1.2.2                 
## [11] GenomeInfoDbData_1.2.6      Rsamtools_2.8.0            
## [13] yaml_2.2.1                  progress_1.2.2             
## [15] pillar_1.6.2                RSQLite_2.2.8              
## [17] lattice_0.20-45             glue_1.4.2                 
## [19] digest_0.6.27               XVector_0.32.0             
## [21] htmltools_0.5.2             Matrix_1.3-4               
## [23] XML_3.99-0.7                pkgconfig_2.0.3            
## [25] biomaRt_2.48.3              zlibbioc_1.38.0            
## [27] purrr_0.3.4                 BiocParallel_1.26.2        
## [29] tibble_3.1.4                KEGGREST_1.32.0            
## [31] generics_0.1.0              ellipsis_0.3.2             
## [33] cachem_1.0.6                SummarizedExperiment_1.22.0
## [35] magrittr_2.0.1              crayon_1.4.1               
## [37] memoise_2.0.0               evaluate_0.14              
## [39] fansi_0.5.0                 xml2_1.3.2                 
## [41] tools_4.1.1                 prettyunits_1.1.1          
## [43] hms_1.1.0                   BiocIO_1.2.0               
## [45] lifecycle_1.0.0             matrixStats_0.60.1         
## [47] stringr_1.4.0               DelayedArray_0.18.0        
## [49] Biostrings_2.60.2           compiler_4.1.1             
## [51] jquerylib_0.1.4             rlang_0.4.11               
## [53] grid_4.1.1                  RCurl_1.98-1.4             
## [55] rjson_0.2.20                rappdirs_0.3.3             
## [57] bitops_1.0-7                rmarkdown_2.11             
## [59] restfulr_0.0.13             DBI_1.1.1                  
## [61] curl_4.3.2                  R6_2.5.1                   
## [63] GenomicAlignments_1.28.0    knitr_1.34                 
## [65] rtracklayer_1.52.1          fastmap_1.1.0              
## [67] bit_4.0.4                   utf8_1.2.2                 
## [69] filelock_1.0.2              stringi_1.7.4              
## [71] Rcpp_1.0.7                  vctrs_0.3.8                
## [73] png_0.1-7                   dbplyr_2.1.1               
## [75] tidyselect_1.1.1            xfun_0.26