Source: https://github.com/markziemann/fran_mbd/blob/master/main_report_integration.Rmd

Introduction

I will perform a multi-contrast pathway analysis involving RNA expression and DNA methylation data looking at differences caused by acetate and high fibre diet.

suppressPackageStartupMessages({
    # to be run in R4
    library("mitch")
})

Import profiling data

Importing the DESeq2 tables I generated earlier.

rna_heart_ctrl_vs_acetate <- read.table("heart_ctrl_vs_acetate_rna.tsv")
rna_heart_ctrl_vs_hifibre <- read.table("heart_ctrl_vs_hifibre_rna.tsv")
rna_spleen_ctrl_vs_acetate <- read.table("spleen_ctrl_vs_acetate_rna.tsv")
rna_spleen_ctrl_vs_hifibre <- read.table("spleen_ctrl_vs_hifibre_rna.tsv")

meth_heart_ctrl_vs_acetate <- read.table("heart_ctrl_vs_acetate_meth.tsv")
meth_heart_ctrl_vs_hifibre <- read.table("heart_ctrl_vs_hifibre_meth.tsv")
meth_spleen_ctrl_vs_acetate <- read.table("spleen_ctrl_vs_acetate_meth.tsv")
meth_spleen_ctrl_vs_hifibre <- read.table("spleen_ctrl_vs_hifibre_meth.tsv")

# strip the gene names out to make downstream analysis easier
rownames(rna_heart_ctrl_vs_acetate) <- sapply(strsplit(rownames(rna_heart_ctrl_vs_acetate),"_"),"[[",1)
rownames(rna_heart_ctrl_vs_hifibre) <- sapply(strsplit(rownames(rna_heart_ctrl_vs_hifibre),"_"),"[[",1)
rownames(rna_spleen_ctrl_vs_acetate) <- sapply(strsplit(rownames(rna_spleen_ctrl_vs_acetate),"_"),"[[",1)
rownames(rna_spleen_ctrl_vs_hifibre) <- sapply(strsplit(rownames(rna_spleen_ctrl_vs_hifibre),"_"),"[[",1)

rownames(meth_heart_ctrl_vs_acetate) <- sapply(strsplit(rownames(meth_heart_ctrl_vs_acetate),"_"),"[[",1)
rownames(meth_heart_ctrl_vs_hifibre) <- sapply(strsplit(rownames(meth_heart_ctrl_vs_hifibre),"_"),"[[",1)
rownames(meth_spleen_ctrl_vs_acetate) <- sapply(strsplit(rownames(meth_spleen_ctrl_vs_acetate),"_"),"[[",1)
rownames(meth_spleen_ctrl_vs_hifibre) <- sapply(strsplit(rownames(meth_spleen_ctrl_vs_hifibre),"_"),"[[",1)

Pathway level analysis with mitch

First fetch gene sets from Reactome.

# gene sets
download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip", 
    destfile="ReactomePathways.gmt.zip")
unzip("ReactomePathways.gmt.zip",overwrite = TRUE)
genesets <- gmt_import("ReactomePathways.gmt")

# gene table
m2h <- read.table("mouse2human.txt.sort")
m2h[,1]=NULL

Heart: ctrl vs acetate

x <- list("rna"=rna_heart_ctrl_vs_acetate,"meth"=meth_heart_ctrl_vs_acetate)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)
## Note: Mean no. genes in input = 23118.5
## Note: no. genes in output = 11707
## Note: estimated proportion of input genes in output = 0.506
capture.output(
    res <- mitch_calc(m,genesets=genesets,priority="effect")
    , file = "/dev/null", append = FALSE,
    type = c("output", "message"), split = FALSE)
## Note: Enrichments with large effect sizes may not be 
##             statistically significant.
head(res$enrichment_result,20)
##                                                                               set
## 315                                    Establishment of Sister Chromatid Cohesion
## 625                                                 Mitotic Telophase/Cytokinesis
## 414                                                               Glucuronidation
## 1215                                                       Viral mRNA Translation
## 744                                                      Peptide chain elongation
## 193                            Constitutive Signaling by NOTCH1 HD Domain Mutants
## 1025                              Signaling by NOTCH1 HD Domain Mutants in Cancer
## 976                                                      Selenocysteine synthesis
## 271                                                    Dissolution of Fibrin Clot
## 48                                      Activation of the pre-replicative complex
## 928                           Response of EIF2AK4 (GCN2) to amino acid deficiency
## 320                                            Eukaryotic Translation Termination
## 203                       Cyclin A/B1/B2 associated events during G2/M transition
## 225                                                         DNA strand elongation
## 318                                             Eukaryotic Translation Elongation
## 455                                                              Heme degradation
## 864              Recognition of DNA damage by PCNA-containing replication complex
## 617                                                                     Mitophagy
## 682  Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
## 356                                      Formation of a pool of free 40S subunits
##      setSize      pMANOVA       s.rna      s.meth        p.rna       p.meth
## 315       10 4.253900e-04  0.71390955  0.11997948 9.251346e-05 5.113032e-01
## 625       10 5.543468e-04  0.68509874  0.20415491 1.757346e-04 2.637228e-01
## 414       11 4.900979e-04  0.56031588  0.40832919 1.292567e-03 1.904774e-02
## 1215      37 2.917320e-11  0.62740221 -0.18306584 3.972917e-11 5.415247e-02
## 744       37 1.121378e-10  0.61430325 -0.16367216 1.000118e-10 8.514360e-02
## 193       10 2.481157e-03 -0.46023767  0.41410618 1.174144e-02 2.337857e-02
## 1025      10 2.481157e-03 -0.46023767  0.41410618 1.174144e-02 2.337857e-02
## 976       40 1.803173e-10  0.56703951 -0.20611983 5.454957e-10 2.419159e-02
## 271       10 6.201525e-03  0.51999658  0.28390186 4.411800e-03 1.201261e-01
## 48        26 1.249212e-06  0.59065017  0.01361185 1.856571e-07 9.044275e-01
## 928       44 2.066483e-10  0.57795827 -0.04296805 3.283386e-11 6.222340e-01
## 320       40 2.362539e-09  0.55236565 -0.13956458 1.497944e-09 1.269719e-01
## 203       19 1.172866e-04  0.54433697 -0.12385172 4.002090e-05 3.501912e-01
## 225       26 9.024083e-06  0.54290004 -0.03642997 1.657264e-06 7.479454e-01
## 318       40 1.775977e-08  0.52542642 -0.12594926 8.958190e-09 1.684335e-01
## 455       10 1.066175e-02  0.29040780 -0.45484312 1.118651e-01 1.276432e-02
## 864       21 8.297836e-05  0.51523598 -0.16026503 4.371555e-05 2.037888e-01
## 617       19 3.223508e-04 -0.02049335 -0.53144476 8.771529e-01 6.071578e-05
## 682       41 3.762444e-08  0.51248364 -0.10457740 1.370317e-08 2.469880e-01
## 356       46 4.546524e-09  0.49743664 -0.15668729 5.356992e-09 6.621354e-02
##         s.dist        SD p.adjustMANOVA
## 315  0.7239212 0.4199720   6.295772e-03
## 625  0.7148703 0.3400786   7.611411e-03
## 414  0.6933157 0.1074708   7.086703e-03
## 1215 0.6535646 0.5730875   9.174972e-09
## 744  0.6357335 0.5501117   2.015277e-08
## 193  0.6191144 0.6182545   2.477219e-02
## 1025 0.6191144 0.6182545   2.477219e-02
## 976  0.6033400 0.5467062   2.835490e-08
## 271  0.5924498 0.1669442   5.307155e-02
## 48   0.5908070 0.4080277   4.910963e-05
## 928  0.5795533 0.4390612   2.888484e-08
## 320  0.5697246 0.4892686   2.122910e-07
## 203  0.5582490 0.4724808   2.202187e-03
## 225  0.5441209 0.4096482   2.588103e-04
## 318  0.5403111 0.4605922   1.117089e-06
## 455  0.5396471 0.5269720   7.797954e-02
## 864  0.5395859 0.4776513   1.683658e-03
## 617  0.5318397 0.3612972   5.133130e-03
## 682  0.5230448 0.4363280   1.972148e-06
## 356  0.5215306 0.4625355   3.574704e-07
unlink("heart_ctrl_vs_acetate_integrate.html")
    capture.output(
        mitch_report(res,outfile=paste("heart_ctrl_vs_acetate_integrate.html"))
        , file = "/dev/null", append = FALSE,
        type = c("output", "message"), split = FALSE)
## Dataset saved as " /tmp/RtmpYKylDb/./heart_ctrl_vs_acetate_integrate.RData ".
## 
## 
## processing file: mitch.Rmd
## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md
## 
## Output created: /tmp/RtmpYKylDb/mitch_report.html

Heart: ctrl vs high fibre

x <- list("rna"=rna_heart_ctrl_vs_hifibre,"meth"=meth_heart_ctrl_vs_hifibre)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)
## Note: Mean no. genes in input = 23496
## Note: no. genes in output = 11716
## Note: estimated proportion of input genes in output = 0.499
capture.output(
    res <- mitch_calc(m,genesets=genesets,priority="effect")
    , file = "/dev/null", append = FALSE,
    type = c("output", "message"), split = FALSE)
## Note: Enrichments with large effect sizes may not be 
##             statistically significant.
head(res$enrichment_result,20)
##                                                                           set
## 414                                                           Glucuronidation
## 503                                           Interferon alpha/beta signaling
## 179                         Classical antibody-mediated complement activation
## 486                                          Initial triggering of complement
## 751                                Phosphorylation of CD3 and TCR zeta chains
## 542                                                     LGI-ADAM interactions
## 661  Negative regulation of TCF-dependent signaling by WNT ligand antagonists
## 202                                          Creation of C4 and C2 activators
## 985                                                      Signaling by Activin
## 912                                          Removal of the Flap Intermediate
## 717                                                       PI-3K cascade:FGFR2
## 719                                                       PI-3K cascade:FGFR4
## 166                                                  Cholesterol biosynthesis
## 913                        Removal of the Flap Intermediate from the C-strand
## 449                                            HSF1-dependent transactivation
## 788                                Processive synthesis on the lagging strand
## 741                                                  Peptide chain elongation
## 956                         STING mediated induction of host immune responses
## 467    IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
## 1118             TRAF6-mediated induction of TAK1 complex within TLR4 complex
##      setSize      pMANOVA      s.rna      s.meth        p.rna       p.meth
## 414       11 2.858383e-05  0.5243835  0.60046600 2.602166e-03 0.0005641229
## 503       42 2.730068e-14  0.6487126 -0.27349136 3.434660e-13 0.0021787923
## 179       10 6.737190e-04  0.6836152 -0.13919358 1.815204e-04 0.4460616028
## 486       19 1.212503e-06  0.6137561 -0.31759380 3.628085e-06 0.0165808118
## 751       10 1.647562e-03  0.6374338 -0.14416539 4.822738e-04 0.4299860274
## 542       11 9.862501e-04 -0.5934604 -0.26107724 6.542865e-04 0.1338782267
## 661       10 2.053361e-03 -0.6328635  0.10954212 5.294930e-04 0.5487252619
## 202       12 1.552352e-03  0.5847573 -0.13170711 4.526898e-04 0.4296655493
## 985       10 5.057947e-03 -0.5267897  0.27314198 3.922616e-03 0.1348274406
## 912       11 3.118552e-03  0.4385771 -0.39613996 1.179151e-02 0.0229304925
## 717       14 8.001451e-04 -0.5112557  0.27909759 9.271195e-04 0.0706670181
## 719       11 3.921024e-03 -0.5106054  0.27351947 3.367297e-03 0.1163157862
## 166       20 4.460525e-05 -0.5386029 -0.21130301 3.052152e-05 0.1019930216
## 913       12 2.804901e-03  0.4805195 -0.30859820 3.953563e-03 0.0642302094
## 449       26 3.162169e-06 -0.5599263 -0.10909390 7.744726e-07 0.3358798943
## 788       12 3.089530e-03  0.4761050 -0.30674698 4.298819e-03 0.0658452517
## 741       37 2.921664e-08  0.5578157  0.04620675 4.322418e-09 0.6269674378
## 956       11 6.756873e-03  0.4333346 -0.33872083 1.283870e-02 0.0517943768
## 467       11 7.153838e-03 -0.3417498  0.42691934 4.973532e-02 0.0142315088
## 1118      11 7.153838e-03 -0.3417498  0.42691934 4.973532e-02 0.0142315088
##         s.dist         SD p.adjustMANOVA
## 414  0.7972061 0.05379844   8.756414e-04
## 503  0.7040068 0.65209670   3.428965e-11
## 179  0.6976422 0.58181369   1.191818e-02
## 486  0.6910589 0.65856384   9.518151e-05
## 751  0.6535331 0.55267408   2.200756e-02
## 542  0.6483492 0.23503042   1.638541e-02
## 661  0.6422738 0.52496004   2.578074e-02
## 202  0.5994063 0.50661688   2.142588e-02
## 985  0.5933919 0.56563710   4.410295e-02
## 912  0.5909964 0.59023412   3.291513e-02
## 717  0.5824756 0.55886418   1.376688e-02
## 719  0.5792502 0.55446003   3.903370e-02
## 166  0.5785690 0.23143600   1.273277e-03
## 913  0.5710795 0.55799046   3.076739e-02
## 449  0.5704550 0.31878665   1.497571e-04
## 788  0.5663654 0.55355997   3.288516e-02
## 741  0.5597262 0.36176217   5.242299e-06
## 956  0.5500097 0.54592565   5.304145e-02
## 467  0.5468575 0.54353119   5.512405e-02
## 1118 0.5468575 0.54353119   5.512405e-02
unlink("heart_ctrl_vs_hifibre_integrate.html")
    capture.output(
        mitch_report(res,outfile=paste("heart_ctrl_vs_hifibre_integrate.html"))
        , file = "/dev/null", append = FALSE,
        type = c("output", "message"), split = FALSE)
## Dataset saved as " /tmp/RtmpYKylDb/./heart_ctrl_vs_hifibre_integrate.RData ".
## 
## 
## processing file: mitch.Rmd
## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md
## 
## Output created: /tmp/RtmpYKylDb/mitch_report.html

Spleen: ctrl vs acetate

x <- list("rna"=rna_spleen_ctrl_vs_acetate,"meth"=meth_spleen_ctrl_vs_acetate)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)
## Note: Mean no. genes in input = 19833.5
## Note: no. genes in output = 10950
## Note: estimated proportion of input genes in output = 0.552
capture.output(
    res <- mitch_calc(m,genesets=genesets,priority="effect")
    , file = "/dev/null", append = FALSE,
    type = c("output", "message"), split = FALSE)
## Note: Enrichments with large effect sizes may not be 
##             statistically significant.
head(res$enrichment_result,20)
##                                                                  set setSize
## 542                                         Leading Strand Synthesis      12
## 754                                             Polymerase switching      12
## 220                                            DNA strand elongation      23
## 538                                         Lagging Strand Synthesis      16
## 481  Inhibition of replication initiation of damaged DNA by RB1/E2F1      12
## 598          Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)      12
## 778                       Processive synthesis on the lagging strand      12
## 902                                 Removal of the Flap Intermediate      11
## 390                                  GP1b-IX-V activation signalling      10
## 287                       E2F mediated regulation of DNA replication      18
## 703                   PCNA-Dependent Long Patch Base Excision Repair      15
## 1160                                   Translesion Synthesis by POLH      10
## 597           Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)      12
## 452                                                Heme biosynthesis      11
## 1209          WNT5A-dependent internalization of FZD2, FZD5 and ROR2      12
## 596                                                  Mismatch Repair      13
## 184                             Condensation of Prophase Chromosomes      10
## 381                                      G1/S-Specific Transcription      23
## 484                  Initiation of Nuclear Envelope (NE) Reformation      14
## 399          Gap-filling DNA repair synthesis and ligation in GG-NER      17
##           pMANOVA      s.rna      s.meth        p.rna      p.meth    s.dist
## 542  1.023463e-05  0.7945846  0.08110867 1.871533e-06 0.626731502 0.7987136
## 754  1.023463e-05  0.7945846  0.08110867 1.871533e-06 0.626731502 0.7987136
## 220  3.417504e-10  0.7922975 -0.06909490 4.699666e-11 0.566454359 0.7953046
## 538  6.646676e-07  0.7659022  0.07611579 1.125181e-07 0.598260670 0.7696752
## 481  3.245906e-05  0.6702551  0.35087920 5.811151e-05 0.035370264 0.7565435
## 598  4.042528e-05  0.7278448  0.17705857 1.264978e-05 0.288383120 0.7490713
## 778  4.889778e-05  0.7399738  0.06098007 9.042008e-06 0.714634281 0.7424822
## 902  1.210500e-04  0.7393978 -0.01608091 2.169936e-05 0.926443107 0.7395727
## 390  4.992354e-04 -0.7095064  0.06378428 1.022258e-04 0.726967372 0.7123677
## 287  1.499458e-06  0.5502348  0.43833089 5.320013e-05 0.001287253 0.7034858
## 703  2.466545e-05  0.6602835  0.18657522 9.521771e-06 0.211069880 0.6861375
## 1160 8.834401e-04  0.6343510  0.25533821 5.137997e-04 0.162170428 0.6838120
## 597  2.911563e-04  0.6505912  0.16838849 9.527545e-05 0.312646021 0.6720295
## 452  6.772728e-04  0.6146731  0.25168496 4.157868e-04 0.148458563 0.6642050
## 1209 3.694786e-04  0.5223380  0.40577193 1.732331e-03 0.014959899 0.6614287
## 596  3.059112e-04  0.6118469  0.19961176 1.336954e-04 0.212861041 0.6435848
## 184  2.071378e-03  0.4140585  0.48886654 2.339858e-02 0.007438631 0.6406520
## 381  7.671459e-07  0.6193394  0.15537500 2.722206e-07 0.197332998 0.6385317
## 484  1.908814e-04  0.5789529  0.26750444 1.765383e-04 0.083195380 0.6377657
## 399  4.616548e-05  0.6098482  0.13853902 1.341697e-05 0.322904225 0.6253862
##              SD p.adjustMANOVA
## 542  0.50450369   9.801627e-05
## 754  0.50450369   9.801627e-05
## 220  0.60909641   1.519569e-08
## 538  0.48775267   8.443992e-06
## 481  0.22583285   2.767913e-04
## 598  0.38946469   3.289508e-04
## 778  0.48012107   3.757885e-04
## 902  0.53420413   8.514532e-04
## 390  0.54679908   2.864277e-03
## 287  0.07912800   1.761156e-05
## 703  0.33496233   2.241495e-04
## 1160 0.26800252   4.640856e-03
## 597  0.34096881   1.840049e-03
## 452  0.25667138   3.682116e-03
## 1209 0.08242468   2.243906e-03
## 596  0.29149424   1.913867e-03
## 184  0.05289728   1.011320e-02
## 381  0.32807238   9.647441e-06
## 484  0.22022729   1.291562e-03
## 399  0.33326593   3.637723e-04
unlink("spleen_ctrl_vs_acetate_integrate.html")
    capture.output(
        mitch_report(res,outfile=paste("spleen_ctrl_vs_acetate_integrate.html"))
        , file = "/dev/null", append = FALSE,
        type = c("output", "message"), split = FALSE)
## Dataset saved as " /tmp/RtmpYKylDb/./spleen_ctrl_vs_acetate_integrate.RData ".
## 
## 
## processing file: mitch.Rmd
## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md
## 
## Output created: /tmp/RtmpYKylDb/mitch_report.html

Spleen: ctrl vs high fibre

x <- list("rna"=rna_spleen_ctrl_vs_hifibre,"meth"=meth_spleen_ctrl_vs_hifibre)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)
## Note: Mean no. genes in input = 19728.5
## Note: no. genes in output = 10887
## Note: estimated proportion of input genes in output = 0.552
capture.output(
    res <- mitch_calc(m,genesets=genesets,priority="effect")
    , file = "/dev/null", append = FALSE,
    type = c("output", "message"), split = FALSE)
## Note: Enrichments with large effect sizes may not be 
##             statistically significant.
head(res$enrichment_result,20)
##                                                              set setSize
## 171            Classical antibody-mediated complement activation      10
## 325                                              FCGR activation      15
## 194                             Creation of C4 and C2 activators      14
## 480                             Initial triggering of complement      20
## 251                                                    Digestion      12
## 640              Na+/Cl- dependent neurotransmitter transporters      11
## 252                                     Digestion and absorption      13
## 158                                     Cholesterol biosynthesis      16
## 963                Signal regulatory protein family interactions      11
## 385            GABA synthesis, release, reuptake and degradation      11
## 863                                 Regulation of IFNA signaling      10
## 1207                                             eNOS activation      10
## 935  SRP-dependent cotranslational protein targeting to membrane      42
## 859                             Regulation of Complement cascade      30
## 166                                Citric acid cycle (TCA cycle)      13
## 578   Metabolism of nitric oxide: NOS3 activation and regulation      14
## 914                           Retrograde neurotrophin signalling      12
## 432                                    HDMs demethylate histones      15
## 440                           HIV elongation arrest and recovery      15
## 727                       Pausing and recovery of HIV elongation      15
##           pMANOVA      s.rna      s.meth        p.rna      p.meth    s.dist
## 171  1.440546e-06  0.8636021 -0.37528730 2.246779e-06 0.039922271 0.9416205
## 325  3.167540e-05  0.6258339 -0.25336645 2.710190e-05 0.089436059 0.6751760
## 194  7.724307e-05  0.6427586 -0.18533458 3.126481e-05 0.230048196 0.6689451
## 480  2.624851e-06  0.6376001 -0.13938529 7.954289e-07 0.280772030 0.6526577
## 251  5.736317e-04 -0.6355862  0.09504981 1.377077e-04 0.568729738 0.6426541
## 640  1.371495e-03 -0.6170049  0.12879067 3.952322e-04 0.459666224 0.6303032
## 252  7.454799e-04 -0.5925638  0.12693652 2.163763e-04 0.428264281 0.6060072
## 158  3.557312e-04 -0.5748551 -0.03639270 6.869038e-05 0.801101283 0.5760059
## 963  3.987849e-03  0.4274549 -0.38382260 1.411361e-02 0.027540414 0.5744889
## 385  7.316149e-03 -0.5431475  0.04904878 1.815232e-03 0.778258218 0.5453577
## 863  1.310116e-02  0.4554840  0.29281052 1.264148e-02 0.108942807 0.5414829
## 1207 1.202383e-02  0.1608900 -0.51622690 3.784584e-01 0.004707644 0.5407178
## 935  2.000991e-08  0.5166831  0.13079980 6.940745e-09 0.142840913 0.5329822
## 859  2.801145e-06  0.4901354 -0.20331583 3.397638e-06 0.054091018 0.5306317
## 166  4.287069e-03 -0.5187391 -0.11165660 1.203717e-03 0.485923865 0.5306199
## 578  2.608992e-03  0.1694630 -0.50220073 2.724474e-01 0.001142110 0.5300220
## 914  6.512644e-03  0.2135785 -0.48076628 2.003110e-01 0.003936237 0.5260723
## 432  2.192129e-03 -0.5208364  0.02609762 4.793356e-04 0.861136559 0.5214898
## 440  3.507006e-03 -0.3737062 -0.34009075 1.223673e-02 0.022617397 0.5052900
## 727  3.507006e-03 -0.3737062 -0.34009075 1.223673e-02 0.022617397 0.5052900
##              SD p.adjustMANOVA
## 171  0.87602710   1.110121e-04
## 325  0.62168856   1.346751e-03
## 194  0.58555030   2.506334e-03
## 480  0.54941162   1.804304e-04
## 251  0.51663768   1.040129e-02
## 640  0.52735711   1.951850e-02
## 252  0.50876353   1.259146e-02
## 158  0.38075043   7.582375e-03
## 963  0.57365985   3.841420e-02
## 385  0.41874604   5.895955e-02
## 863  0.11502756   8.731748e-02
## 1207 0.47879392   8.236321e-02
## 935  0.27286072   2.242929e-06
## 859  0.49034407   1.817796e-04
## 166  0.28785081   4.004512e-02
## 578  0.47493800   3.153811e-02
## 914  0.49097594   5.375903e-02
## 432  0.38674075   2.786490e-02
## 440  0.02376968   3.487208e-02
## 727  0.02376968   3.487208e-02
unlink("spleen_ctrl_vs_hifibre_integrate.html")
    capture.output(
        mitch_report(res,outfile=paste("spleen_ctrl_vs_hifibre_integrate.html"))
        , file = "/dev/null", append = FALSE,
        type = c("output", "message"), split = FALSE)
## Dataset saved as " /tmp/RtmpYKylDb/./spleen_ctrl_vs_hifibre_integrate.RData ".
## 
## 
## processing file: mitch.Rmd
## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md
## 
## Output created: /tmp/RtmpYKylDb/mitch_report.html

End of report

Session information

sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pkgload_1.1.0   GGally_2.0.0    ggplot2_3.3.2   reshape2_1.4.4 
##  [5] beeswarm_0.2.3  gplots_3.0.3    gtools_3.8.2    tibble_3.0.1   
##  [9] dplyr_1.0.0     echarts4r_0.3.2 mitch_1.0.6    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6       assertthat_0.2.1   rprojroot_1.3-2    digest_0.6.25     
##  [5] mime_0.9           R6_2.4.1           plyr_1.8.6         backports_1.1.8   
##  [9] evaluate_0.14      highr_0.8          pillar_1.4.4       rlang_0.4.6       
## [13] gdata_2.18.0       rmarkdown_2.3      desc_1.2.0         labeling_0.3      
## [17] stringr_1.4.0      htmlwidgets_1.5.1  munsell_0.5.0      shiny_1.5.0       
## [21] compiler_4.0.2     httpuv_1.5.4       xfun_0.15          pkgconfig_2.0.3   
## [25] htmltools_0.5.0    tidyselect_1.1.0   gridExtra_2.3      reshape_0.8.8     
## [29] crayon_1.3.4       withr_2.2.0        later_1.1.0.1      MASS_7.3-51.6     
## [33] bitops_1.0-6       grid_4.0.2         jsonlite_1.7.0     xtable_1.8-4      
## [37] gtable_0.3.0       lifecycle_0.2.0    magrittr_1.5       scales_1.1.1      
## [41] KernSmooth_2.23-17 stringi_1.4.6      farver_2.0.3       promises_1.1.1    
## [45] testthat_2.3.2     ellipsis_0.3.1     generics_0.0.2     vctrs_0.3.1       
## [49] pbmcapply_1.5.0    RColorBrewer_1.1-2 tools_4.0.2        glue_1.4.1        
## [53] purrr_0.3.4        parallel_4.0.2     fastmap_1.0.1      yaml_2.2.1        
## [57] colorspace_1.4-1   caTools_1.18.0     knitr_1.29