Introduction

Previously, Mandhri and I analysed the B-PROOF 450K data, trying to understand whether vitamin supplementation caused changes in gene methylation. We used Limma and some basic analyses, which showed no specific probes with FDR<0.05, nor any DMRs.

In this analysis we will use the principle of Gene Set Enrichment Analysis, applying it to many probes belonging to genes. If the probes are trending in concert, then we can make some judgement about the enrichment of those probes. The statistical test used is the Wilcox test, which can be applied to competitive or self contained test types.

library("parallel")
library("dplyr")
library("kableExtra")
library("eulerr")
library("mitch")
library("tictoc")
source("meth_functions.R")

CORES= detectCores()/2

Get array annotation data

anno <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
myann <- data.frame(anno[,c("UCSC_RefGene_Name","Regulatory_Feature_Group","Islands_Name","Relation_to_Island")])
promoters <- grep("Prom",myann$Regulatory_Feature_Group)

Load Estill data

nat_vs_fh <- readRDS("estill_nat_vs_fh.rds")
fh_vs_fz <- readRDS("estill_fh_vs_fz.rds")
nat_vs_fx <- readRDS("estill_nat_vs_fx.rds")
nat_vs_fz <- readRDS("estill_nat_vs_fz.rds")
iui_vs_fx <- readRDS("estill_iui_vs_fx.rds")
nat_vs_iui <- readRDS("estill_nat_vs_iui.rds")

if ( ! file.exists("ReactomePathways.gmt") ) {
  download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip",
    destfile="ReactomePathways.gmt.zip")
  unzip("ReactomePathways.gmt.zip")
}
file.info("ReactomePathways.gmt")
##                        size isdir mode               mtime               ctime
## ReactomePathways.gmt 897680 FALSE  664 2022-06-08 15:37:39 2022-06-08 15:37:39
##                                    atime  uid  gid uname grname
## ReactomePathways.gmt 2022-06-11 21:21:46 1001 1001   mdz    mdz
genesets <- gmt_import("ReactomePathways.gmt")
length(genesets)
## [1] 2546

Nat vs fh

dm <- nat_vs_fh$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
321265 cg20757019 Unclassified chr2:95872891-95873548 Island -1.2204194 -4.112831 -22.28318 0 0 71.72984 T C
138436 cg08260549 XPO7;XPO7 Promoter_Associated chr8:21776842-21777942 Island -0.9881965 -4.154736 -19.07579 0 0 61.62133 T C
268273 cg16905586 GMPPB;GMPPB;GMPPB;GMPPB Promoter_Associated chr3:49760863-49761895 Island -0.7473933 -3.581648 -19.06919 0 0 61.59920 T C
34194 cg01931797 KCTD21;USP35 Promoter_Associated chr11:77899564-77899990 Island -1.0105356 -4.476141 -18.49684 0 0 59.65971 T C
132599 cg07897831 CASKIN2;TSEN54 Unclassified chr17:73511016-73513176 Island -0.8859771 -4.316226 -18.48519 0 0 59.61979 T C
286730 cg18233405 TSPYL5;TSPYL5 Promoter_Associated chr8:98289604-98290404 Island -0.9289544 -4.609038 -18.30959 0 0 59.01588 T C
234473 cg14572967 CD72 Promoter_Associated chr9:35616980-35617324 Island -1.0332411 -4.645348 -18.13178 0 0 58.40020 T C
66567 cg03817939 FAM176A;FAM176A chr2:75787717-75788312 Island -0.9779883 -4.231985 -17.88437 0 0 57.53653 T C
26062 cg01447112 Unclassified_Cell_type_specific chr7:6703503-6704075 Island -1.0159553 -3.733925 -17.72041 0 0 56.95970 T C
221706 cg13871588 MEA1;KLHDC3 Promoter_Associated chr6:42981408-42982077 Island -0.9076831 -4.761842 -17.60113 0 0 56.53776 T C
395222 cg26206990 APH1B;APH1B chr15:63569296-63570100 Island -0.9167084 -3.052166 -17.52566 0 0 56.26983 T C
51218 cg02916102 CYP11A1;CYP11A1;CYP11A1 Unclassified_Cell_type_specific chr15:74658038-74658574 Island -0.9826454 -4.386873 -17.42301 0 0 55.90413 T C
121274 cg07177569 ITGAV;ITGAV Promoter_Associated chr2:187454399-187455349 Island -0.5947721 -3.715024 -17.24021 0 0 55.24939 T C
312054 cg20064047 ASH1L;LOC645676 Promoter_Associated chr1:155531914-155533280 Island -1.0331504 -4.653254 -17.23125 0 0 55.21719 T C
63905 cg03655371 chr5:134827285-134827644 Island -0.9109321 -4.035717 -17.19908 0 0 55.10145 T C
207083 cg12950624 RTN2;RTN2;RTN2;RTN2 Unclassified chr19:45999761-46000210 Island -1.0184699 -3.613885 -17.16799 0 0 54.98946 T C
195450 cg12089543 C22orf40 Unclassified chr22:46645764-46646957 Island -0.8208395 -4.527876 -17.01215 0 0 54.42621 T C
179618 cg10992925 SEMA3F Unclassified chr3:50191971-50193130 Island -0.7506680 -3.275289 -16.91302 0 0 54.06616 T C
196471 cg12159575 UHRF1;UHRF1 Promoter_Associated chr19:4909262-4910256 S_Shore -1.0349440 -4.558812 -16.84753 0 0 53.82758 T C
372380 cg24543097 RBCK1;RBCK1 Promoter_Associated chr20:388472-389342 Island -0.8354551 -3.997386 -16.51521 0 0 52.60788 T C
342396 cg22394521 DIDO1;DIDO1;C20orf11;DIDO1 Promoter_Associated chr20:61568678-61569916 Island -0.9078579 -4.374544 -16.39364 0 0 52.15788 T C
364043 cg23963136 CD320;CD320 Promoter_Associated chr19:8372597-8373302 Island -1.1018554 -4.724252 -16.38992 0 0 52.14406 T C
359726 cg23649004 KCNJ4 chr22:38850766-38851285 S_Shore -0.9915855 -4.030695 -16.35127 0 0 52.00055 T C
291292 cg18555811 HES1 Unclassified chr3:193854575-193856015 N_Shore -1.0194080 -4.418749 -16.19820 0 0 51.43019 T C
48905 cg02779429 MGC23284;SNAI3 Promoter_Associated chr16:88752520-88753278 Island -0.5899063 -3.762682 -16.08243 0 0 50.99668 T C
313863 cg20206224 POLH;XPO5;XPO5 Promoter_Associated chr6:43543124-43544076 Island -0.7537092 -4.170925 -16.04315 0 0 50.84918 T C
116889 cg06931446 ARHGEF18 Unclassified chr19:7459779-7460376 Island -0.8893787 -3.856002 -16.02293 0 0 50.77313 T C
110655 cg06571075 MACROD2 chr20:13975768-13976287 Island -1.0259810 -4.618269 -16.01764 0 0 50.75326 T C
323682 cg20958497 Promoter_Associated chr19:18058664-18059218 Island -0.8294587 -4.665326 -15.99199 0 0 50.65673 T C
80305 cg04645421 Unclassified chr5:108063600-108064072 Island -0.6196834 -4.047378 -15.96752 0 0 50.56454 T C
255870 cg16080015 RBAK Promoter_Associated chr7:5085411-5086342 Island -0.8446048 -4.312135 -15.93617 0 0 50.44634 T C
267712 cg16863872 PWP2 Promoter_Associated chr21:45526956-45527813 Island -0.8823532 -4.506239 -15.92953 0 0 50.42128 T C
202957 cg12636108 GPRIN1 Unclassified chr5:176036458-176037557 Island -0.8827711 -4.277420 -15.87376 0 0 50.21060 T C
346062 cg22686066 TAF4 Promoter_Associated chr20:60640721-60641805 Island -0.6879501 -3.594290 -15.86896 0 0 50.19247 T C
95181 cg05563672 TMPRSS2;TMPRSS2;TMPRSS2 chr21:42878751-42880674 Island -0.7711359 -3.858087 -15.85695 0 0 50.14703 T C
267523 cg16849041 DOCK5;DOCK5 chr8:25041795-25042820 Island -0.9716089 -4.423697 -15.75993 0 0 49.77927 T C
53132 cg03023152 GRHL2 chr8:102505512-102506430 Island -0.5973373 -3.429569 -15.73591 0 0 49.68802 T C
235315 cg14618681 E2F1 Promoter_Associated chr20:32273557-32274505 Island -1.0242459 -4.506148 -15.64425 0 0 49.33908 T C
313948 cg20213228 chr20:61806254-61810867 Island -1.0769030 -4.652884 -15.53641 0 0 48.92709 T C
176371 cg10769393 ZNF554 Promoter_Associated chr19:2819630-2820295 Island -1.0680501 -3.778827 -15.48963 0 0 48.74787 T C
388254 cg25692259 FARSB Promoter_Associated chr2:223520516-223520893 Island -0.5923327 -3.500473 -15.48860 0 0 48.74389 T C
274198 cg17331738 NES Unclassified chr1:156646292-156647260 Island -0.7325151 -3.831646 -15.39768 0 0 48.39469 T C
356043 cg23375190 ADRBK2 Promoter_Associated chr22:25960959-25961368 N_Shore -0.7117320 -4.208506 -15.36853 0 0 48.28249 T C
324400 cg21007089 INO80;INO80 Promoter_Associated chr15:41408059-41408856 Island -0.6445564 -3.220404 -15.35825 0 0 48.24288 T C
146559 cg08793877 chr2:71115927-71116412 Island -0.5726253 -3.019430 -15.31507 0 0 48.07640 T C
5060 cg00275962 POLR1C;YIPF3;POLR1C;POLR1C;POLR1C Promoter_Associated chr6:43484561-43484887 Island -0.9752373 -4.168924 -15.24634 0 0 47.81088 T C
266554 cg16774013 NFATC1;NFATC1;NFATC1;NFATC1;NFATC1 chr18:77153292-77160759 Island -1.0102845 -2.806940 -15.18816 0 0 47.58561 T C
260863 cg16415121 ORC3L;ORC3L;RARS2 Promoter_Associated chr6:88299620-88299945 Island -0.9024171 -4.480371 -15.17342 0 0 47.52847 T C
6274 cg00342743 VDAC2;VDAC2 Unclassified chr10:76969992-76971002 Island -0.6593920 -3.056110 -15.06331 0 0 47.10061 T C
381817 cg25214684 AKIRIN1;AKIRIN1 Promoter_Associated chr1:39456655-39457271 Island -0.8254238 -4.903603 -14.99170 0 0 46.82149 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc() 
## 69.108 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_nat_vs_fh.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
TNXB 543 -1.7550694 -2.0239062 0 48.752142 0.00e+00
COL11A2 226 -1.9345239 -2.0118850 0 20.625766 0.00e+00
PRDM16 608 -0.9229984 -0.9313451 0 19.072005 0.00e+00
GNAS 190 -1.9135160 -1.6526126 0 18.262111 0.00e+00
GALNT9 234 -1.4875982 -1.6497210 0 17.000055 0.00e+00
KCNQ1 302 -1.1824793 -1.0542824 0 16.033252 0.00e+00
TP73 123 -2.3910989 -2.6022255 0 15.762783 0.00e+00
HCCA2 245 -1.3607826 -1.2106614 0 14.465927 0.00e+00
CACNA1H 159 -1.6636723 -1.4533296 0 13.621682 0.00e+00
SGCE 88 -1.9604948 -1.7674491 0 12.784624 0.00e+00
OBSCN 127 -1.8587545 -1.8875890 0 12.267947 0.00e+00
GPR123 94 -2.3268001 -2.5113450 0 12.012945 0.00e+00
MEGF6 133 -1.7058410 -1.6645844 0 11.739020 0.00e+00
SLC9A3 102 -2.0223446 -2.1738954 0 11.644141 0.00e+00
VENTX 45 -2.6291003 -2.2431557 0 11.611851 0.00e+00
GNASAS 88 -2.5818448 -2.2719013 0 11.542270 1.00e-07
BAHCC1 109 -1.8023178 -1.7378130 0 11.476015 1.00e-07
SORCS2 186 -1.2258097 -1.2815147 0 11.387671 1.00e-07
RNF39 86 -2.0963577 -2.2911862 0 11.384035 1.00e-07
ZBTB12 76 -2.6089769 -2.7432983 0 11.106987 2.00e-07
INS-IGF2 138 -1.6046411 -1.4679991 0 10.804554 3.00e-07
BAI1 82 -2.2209308 -2.4697111 0 10.581060 5.00e-07
PTPRN2 1197 -0.4301847 -0.4387568 0 10.442732 7.00e-07
PLEC1 145 -1.6463174 -1.8945766 0 10.410070 8.00e-07
ASCL2 49 -2.5963669 -2.8990198 0 10.393183 8.00e-07
SEPT9 160 -1.3519284 -1.6499158 0 10.383312 8.00e-07
CAMTA1 237 -1.1976926 -1.0927495 0 10.329369 9.00e-07
PEG10 105 -1.5903150 -1.3879374 0 10.324669 9.00e-07
ZIC1 46 -1.7470187 -1.7203546 0 10.306050 1.00e-06
BLCAP 119 -1.4396697 -1.4483274 0 10.182219 1.30e-06
H19 61 -3.2955286 -3.6280628 0 9.869585 2.70e-06
HDAC4 405 -0.7286166 -0.7644442 0 9.767580 3.40e-06
BRSK2 103 -1.9049936 -1.9838964 0 9.763405 3.40e-06
RNH1 41 -2.8438976 -2.4330019 0 9.638079 4.60e-06
LOC645323 83 -1.7956804 -1.7889205 0 9.448559 7.10e-06
RGMA 70 -1.7599422 -1.7627157 0 9.241231 1.14e-05
MAD1L1 687 -0.5540562 -0.5655013 0 9.133065 1.47e-05
VAX1 39 -2.5366442 -2.4953138 0 9.123169 1.50e-05
CHD5 75 -2.2860975 -2.3154916 0 9.108626 1.55e-05
PRR5-ARHGAP8 45 -2.8298156 -3.0925158 0 9.074794 1.68e-05
HOXA5 51 -3.1312229 -3.3646735 0 9.044000 1.80e-05
C7orf50 297 -0.8915673 -0.9566438 0 8.991203 2.03e-05
PLCH2 64 -2.5294698 -2.8252694 0 8.926350 2.36e-05
NR4A2 35 -2.6817573 -2.7507699 0 8.837080 2.90e-05
IDUA 44 -2.3567672 -2.5029327 0 8.830580 2.94e-05
ANK1 124 -1.2543713 -1.3510050 0 8.794537 3.19e-05
ZMIZ1 100 -1.5932136 -1.8909942 0 8.745938 3.57e-05
SLC44A4 96 -1.5711781 -1.3628664 0 8.730300 3.70e-05
C6orf27 63 -2.7141860 -2.5638097 0 8.651619 4.44e-05
GGT1 39 -2.4281370 -2.3926057 0 8.632960 4.63e-05 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
395 Expression and translocation of olfactory receptors 311 0.0000000 0.6498075 0.0000000
1490 eNOS activation 11 0.0002076 -0.6458010 0.0050022
840 Olfactory Signaling Pathway 318 0.0000000 0.6334493 0.0000000
1416 Transcriptional regulation of testis differentiation 12 0.0003153 -0.6004648 0.0067409
276 Defective B3GAT3 causes JDSSDHD 17 0.0000303 -0.5841630 0.0012113
277 Defective B4GALT7 causes EDS, progeroid type 17 0.0000470 -0.5700459 0.0015483
712 Metabolism of nitric oxide: NOS3 activation and regulation 15 0.0001447 -0.5665530 0.0037881
1429 Translocation of ZAP-70 to Immunological synapse 17 0.0000627 0.5605734 0.0019820
136 CD28 dependent Vav1 pathway 11 0.0022403 0.5321145 0.0261249
909 Phosphorylation of CD3 and TCR zeta chains 20 0.0000380 0.5319402 0.0013733
130 Butyrophilin (BTN) family interactions 12 0.0014408 0.5311325 0.0195284
658 LGI-ADAM interactions 14 0.0005886 -0.5303993 0.0106376
274 Defective B3GALT6 causes EDSP2 and SEMDJL1 17 0.0001885 -0.5229788 0.0047090
1508 p75NTR recruits signalling complexes 12 0.0022717 -0.5087768 0.0261249
897 Pexophagy 11 0.0037628 -0.5044406 0.0352590
1493 mRNA Editing 10 0.0059665 0.5020711 0.0455134
562 Hormone ligand-binding receptors 12 0.0030219 0.4943285 0.0310859
509 Glucuronidation 19 0.0001955 0.4934857 0.0047872
341 Downregulation of ERBB2:ERBB3 signaling 13 0.0021587 -0.4912768 0.0257725
1 A tetrasaccharide linker sequence is required for GAG synthesis 23 0.0000479 -0.4895886 0.0015483 
#mitch_report(mres,outfile="gmeawg_mitch_nat_vs_fh.html",overwrite=FALSE)
# Promoter
dm <- nat_vs_fh$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
138436 XPO7;XPO7 -19.07579
268273 GMPPB;GMPPB;GMPPB;GMPPB -19.06919
34194 KCTD21;USP35 -18.49684
286730 TSPYL5;TSPYL5 -18.30959
234473 CD72 -18.13178
221706 MEA1;KLHDC3 -17.60113
121274 ITGAV;ITGAV -17.24021
312054 ASH1L;LOC645676 -17.23125
196471 UHRF1;UHRF1 -16.84753
372380 RBCK1;RBCK1 -16.51521
342396 DIDO1;DIDO1;C20orf11;DIDO1 -16.39364
364043 CD320;CD320 -16.38992
48905 MGC23284;SNAI3 -16.08243
313863 POLH;XPO5;XPO5 -16.04315
323682 -15.99199
255870 RBAK -15.93617
267712 PWP2 -15.92953
346062 TAF4 -15.86896
235315 E2F1 -15.64425
176371 ZNF554 -15.48963
388254 FARSB -15.48860
356043 ADRBK2 -15.36853
324400 INO80;INO80 -15.35825
5060 POLR1C;YIPF3;POLR1C;POLR1C;POLR1C -15.24634
260863 ORC3L;ORC3L;RARS2 -15.17342
381817 AKIRIN1;AKIRIN1 -14.99170
389806 ZNF589 -14.84462
307279 UBE2K;UBE2K;UBE2K -14.74420
304268 C14orf43 -14.71084
54325 G3BP2;G3BP2;G3BP2;G3BP2;G3BP2 -14.60602
374812 AGPAT3 -14.57796
32034 PRR7;PRR7 -14.51387
283544 WDR1;WDR1;WDR1;WDR1 -14.49641
55372 HTR7P;HEBP1 -14.48667
358320 FGF9 -14.48205
101775 ERH;SLC39A9 -14.44480
292848 RELL2;RELL2;HDAC3 -14.41945
107155 SLC25A33 -14.41385
398413 IRAK3;IRAK3;IRAK3;IRAK3 -14.39522
11885 RAD54L;RAD54L;RAD54L -14.38503
96919 -14.30852
220041 NAPA;NAPA -14.30640
338499 CCDC28B -14.28347
302499 EGR2;EGR2;EGR2;EGR2 -14.25835
336088 RNF216L;RNF216L;RNF216L -14.25469
329001 GPN1;CCDC121;CCDC121;GPN1;CCDC121;GPN1;GPN1;GPN1 -14.24758
169177 DONSON;DONSON -14.24199
416377 PPAP2A;RNF138P1;PPAP2A -14.21379
252955 PTTG1IP -14.20401
138526 SPRY4;SPRY4 -14.20162 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 31.564 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]] 
write.table(res ,file="estill_gmeapr_nat_vs_fh.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
PEG10 61 -2.633558 -2.560692 0.0e+00 10.664267 0.0000002
SGCE 58 -2.551463 -2.405739 0.0e+00 10.150269 0.0000007
RASA3 34 -2.640865 -2.312837 0.0e+00 9.235020 0.0000060
RPP21 35 -2.354291 -2.490313 0.0e+00 8.193627 0.0000660
HDAC4 37 -2.387258 -2.019193 0.0e+00 7.880911 0.0001356
MGC23284 27 -3.810224 -3.102748 0.0e+00 7.826780 0.0001536
PTEN 53 -2.648795 -2.531096 0.0e+00 7.745124 0.0001854
TRIM27 53 -1.914801 -2.010081 0.0e+00 7.700606 0.0002053
KILLIN 54 -2.582496 -2.521612 0.0e+00 7.682036 0.0002143
ZBTB9 35 -2.418829 -2.325644 0.0e+00 7.584712 0.0002681
FAM50B 29 -3.491873 -3.761613 1.0e-07 7.030900 0.0009595
VARS2 40 -1.618635 -1.269132 2.0e-07 6.786642 0.0016838
ZBTB12 34 -2.698595 -2.554656 2.0e-07 6.762849 0.0017784
FLOT1 68 -2.071915 -2.227315 2.0e-07 6.736051 0.0018914
SNORD48 23 -2.867808 -2.201860 2.0e-07 6.622660 0.0024555
CCHCR1 29 -3.184264 -3.399362 3.0e-07 6.583742 0.0026854
DDAH2 39 -2.431926 -2.782587 3.0e-07 6.535724 0.0029991
TCF19 30 -3.062322 -3.327824 3.0e-07 6.501983 0.0032410
C6orf48 42 -1.888501 -1.837410 4.0e-07 6.446423 0.0036830
PCNA 22 -3.144867 -2.641857 5.0e-07 6.321630 0.0049086
FAM134C 22 -4.030514 -3.867659 5.0e-07 6.321630 0.0049086
TUBG1 22 -4.030514 -3.867659 5.0e-07 6.321630 0.0049086
L3MBTL 22 -2.820024 -2.280554 5.0e-07 6.321630 0.0049086
ST7OT4 22 -2.677325 -2.706105 5.0e-07 6.321630 0.0049086
ST7OT1 22 -2.677325 -2.706105 5.0e-07 6.321630 0.0049086
ST7 22 -2.677325 -2.706105 5.0e-07 6.321630 0.0049086
NFKB2 24 -3.517972 -3.516967 6.0e-07 6.224720 0.0061315
PHF1 28 -3.040643 -2.864176 1.0e-06 5.991089 0.0104992
HLA-E 35 -1.588934 -1.355661 1.1e-06 5.956289 0.0113741
ANKHD1-EIF4EBP3 26 -2.805653 -2.512700 1.3e-06 5.892281 0.0131789
CENPT 29 -3.161402 -2.977406 1.4e-06 5.859466 0.0142120
B3GALT4 50 -1.947170 -2.041465 1.7e-06 5.773581 0.0173179
SKIV2L2 20 -2.863361 -2.151601 1.9e-06 5.719570 0.0196095
DHX29 20 -2.863361 -2.151601 1.9e-06 5.719570 0.0196095
CCDC59 21 -2.078975 -1.559017 1.9e-06 5.719570 0.0196095
C12orf26 21 -2.078975 -1.559017 1.9e-06 5.719570 0.0196095
WRB 21 -2.101794 -2.012610 1.9e-06 5.719570 0.0196095
DOM3Z 49 -1.561319 -1.754114 2.3e-06 5.630673 0.0240520
STK19 49 -1.561319 -1.754114 2.3e-06 5.630673 0.0240520
KIAA1949 67 -1.750038 -1.829740 2.8e-06 5.546250 0.0292072
RAB1B 58 -2.106089 -2.793929 3.0e-06 5.518262 0.0311484
DAXX 38 -1.868030 -1.728899 3.1e-06 5.509534 0.0317776
DNAJC30 19 -3.291147 -2.663646 3.8e-06 5.418540 0.0391808
WBSCR22 19 -3.291147 -2.663646 3.8e-06 5.418540 0.0391808
MGMT 19 -2.976294 -2.268018 3.8e-06 5.418540 0.0391808
MOBKL2A 19 -3.577264 -2.855826 3.8e-06 5.418540 0.0391808
CYP51A1 20 -2.454921 -2.293599 3.8e-06 5.418540 0.0391808
DHRS1 19 -2.748465 -2.369678 3.8e-06 5.418540 0.0391808
C14orf21 19 -2.748465 -2.369678 3.8e-06 5.418540 0.0391808
C7orf50 25 -2.774840 -2.427002 4.2e-06 5.379622 0.0428247 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1077 Termination of O-glycan biosynthesis 10 0.0004588 0.6398331 0.2736008
553 Methylation 10 0.0136966 -0.4502378 0.5009352
313 FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes 14 0.0043411 -0.4403409 0.5009352
516 MAP3K8 (TPL2)-dependent MAPK1/3 activation 13 0.0155106 -0.3877521 0.5009352
1056 TNFR1-induced proapoptotic signaling 12 0.0217553 -0.3826247 0.5009352
972 Signaling by Hippo 11 0.0310743 -0.3755052 0.5334932
142 Cholesterol biosynthesis 20 0.0047474 -0.3648353 0.5009352
1026 Sulfur amino acid metabolism 17 0.0122759 -0.3508958 0.5009352
21 Aberrant regulation of mitotic G1/S transition in cancer due to RB1 defects 15 0.0195645 -0.3482424 0.5009352
212 Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) 15 0.0195645 -0.3482424 0.5009352
279 ERKs are inactivated 11 0.0497721 -0.3416901 0.5920834
447 InlB-mediated entry of Listeria monocytogenes into host cell 11 0.0505143 -0.3405870 0.5920834
1027 Suppression of phagosomal maturation 12 0.0456873 -0.3332201 0.5614359
1022 Spry regulation of FGF signaling 15 0.0281239 -0.3275070 0.5157484
1148 Uptake and actions of bacterial toxins 18 0.0164534 -0.3266742 0.5009352
1138 Triglyceride catabolism 11 0.0634170 -0.3232912 0.6161068
607 Negative regulation of FGFR1 signaling 17 0.0210793 -0.3232209 0.5009352
608 Negative regulation of FGFR2 signaling 17 0.0210793 -0.3232209 0.5009352
609 Negative regulation of FGFR3 signaling 17 0.0210793 -0.3232209 0.5009352
610 Negative regulation of FGFR4 signaling 17 0.0210793 -0.3232209 0.5009352 
#mitch_report(mres,outfile="gmeapr_mitch_nat_vs_fh.html",overwrite=FALSE)
rm(nat_vs_fh)

fh vs fz

dm <- fh_vs_fz$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
216964 cg13601636 FCAR;FCAR;FCAR;FCAR;FCAR;FCAR;FCAR;FCAR;FCAR OpenSea -0.7080566 1.5973963 -9.328265 0 0.0e+00 21.57487 T C
175512 cg10704137 chr6:25732692-25732957 N_Shore -0.5687155 1.6710956 -9.061803 0 0.0e+00 20.48644 T C
338404 cg22078451 PDE4D;PDE4D;PDE4D chr5:58334836-58335881 Island -0.7785473 -3.3146330 -8.800331 0 0.0e+00 19.41488 T C
201535 cg12538597 OpenSea -0.5784615 1.3167580 -8.230334 0 4.0e-07 17.07173 T C
274520 cg17353079 HSPA1L chr6:31782872-31785190 N_Shelf -0.5035957 0.8537704 -8.112780 0 5.0e-07 16.58805 T C
102728 cg06039171 TUBB1 chr20:57599202-57599408 S_Shore -0.3525487 1.6221761 -8.042838 0 5.0e-07 16.30032 T C
384964 cg25444615 OpenSea -0.5833632 0.2079055 -8.009164 0 5.0e-07 16.16181 T C
177259 cg10824722 OpenSea -0.4029930 0.7771542 -8.007771 0 5.0e-07 16.15607 T C
119836 cg07100957 ZNF324 chr19:58982329-58983512 Island -0.4640682 2.1649437 -7.991191 0 5.0e-07 16.08788 T C
84583 cg04902930 CA13 OpenSea -0.3821534 0.8153866 -7.902816 0 6.0e-07 15.72448 T C
22643 cg01249134 chr18:580179-580899 N_Shelf -0.4020978 1.2393025 -7.858062 0 7.0e-07 15.54052 T C
296968 cg18967788 OpenSea -0.3808428 2.6568271 -7.829497 0 7.0e-07 15.42313 T C
235802 cg14648311 OpenSea -0.4010927 1.4346820 -7.813398 0 7.0e-07 15.35698 T C
402190 cg26670636 C7orf61 OpenSea -0.3214439 1.1631114 -7.796676 0 7.0e-07 15.28827 T C
107040 cg06339505 KRT14 OpenSea -0.5286351 2.4460682 -7.794355 0 7.0e-07 15.27874 T C
102834 cg06046629 CACNA1D;CACNA1D;CACNA1D OpenSea -0.4453258 1.0106128 -7.703615 0 8.0e-07 14.90610 T C
144399 cg08645878 SMUG1 Promoter_Associated OpenSea -0.4327914 1.7241031 -7.702697 0 8.0e-07 14.90234 T C
159234 cg09622330 GRIN2A;GRIN2A;GRIN2A OpenSea -0.5667341 2.1465123 -7.694649 0 8.0e-07 14.86930 T C
147204 cg08834050 CUL7;CUL7;MRPL2 chr6:43021125-43021694 S_Shore -0.4830271 2.1232084 -7.666352 0 8.0e-07 14.75316 T C
176800 cg10795676 BTN3A2 OpenSea -0.5659079 2.0116087 -7.665818 0 8.0e-07 14.75098 T C
132127 cg07867325 NonGene_Associated chr3:73159857-73160140 Island -0.4728249 0.7909903 -7.664602 0 8.0e-07 14.74599 T C
40922 cg02322203 HSD11B2 Unclassified_Cell_type_specific chr16:67464388-67465462 Island 0.3401412 -4.7145066 7.643480 0 9.0e-07 14.65932 T C
135219 cg08066417 CDH5 OpenSea -0.5466326 1.3173463 -7.631986 0 9.0e-07 14.61217 T C
24228 cg01345365 OpenSea -0.5130267 1.2806869 -7.616383 0 9.0e-07 14.54817 T C
334190 cg21748749 ZNF610;ZNF610;ZNF610 chr19:52839444-52839937 N_Shore -0.3561904 1.2515972 -7.583034 0 1.0e-06 14.41142 T C
60057 cg03437924 LCMT1;LCMT1 Promoter_Associated chr16:25122810-25123442 Island 0.3902322 -2.9307960 7.578188 0 1.0e-06 14.39155 T C
331281 cg21528620 KCNC4;KCNC4;KCNC4 chr1:110752256-110754794 Island 0.4152673 -3.2196462 7.570231 0 1.0e-06 14.35893 T C
306824 cg19707448 chr17:25783099-25784358 N_Shelf -0.3938671 2.5687638 -7.557811 0 1.0e-06 14.30803 T C
414449 cg27494597 HLA-DPB2 chr6:33084740-33084995 S_Shelf -0.2834770 1.2679978 -7.547282 0 1.0e-06 14.26488 T C
202833 cg12627695 GBX1 Unclassified chr7:150863966-150865511 Island 0.3509641 -2.1373478 7.528127 0 1.1e-06 14.18639 T C
269279 cg16988008 EXPH5 Promoter_Associated chr11:108463598-108464103 Island 0.2410643 -2.6543357 7.436941 0 1.5e-06 13.81303 T C
15240 cg00832928 SELT chr3:150329457-150329728 Island -0.7369165 1.5365035 -7.436525 0 1.5e-06 13.81133 T C
220387 cg13794268 chr9:132331218-132331458 S_Shelf -0.3326726 0.5995177 -7.412144 0 1.6e-06 13.71159 T C
412115 cg27327370 chr2:192746684-192746996 Island -0.4385816 2.4551875 -7.392791 0 1.7e-06 13.63244 T C
43373 cg02466933 YWHAQ Promoter_Associated chr2:9770189-9771562 Island 0.3547699 -1.6303100 7.392156 0 1.7e-06 13.62985 T C
258474 cg16263627 C15orf51 chr15:100339821-100340420 N_Shore -0.3497480 0.3884215 -7.369910 0 1.8e-06 13.53890 T C
168295 cg10217767 DDX11;DDX11;DDX11 OpenSea -0.4335883 1.7872500 -7.364842 0 1.8e-06 13.51819 T C
318554 cg20568408 TDP1;TDP1 chr14:90420900-90421175 S_Shelf -0.2823297 1.6203438 -7.354216 0 1.8e-06 13.47476 T C
134834 cg08040148 chr17:81016044-81016295 S_Shelf -0.4248175 0.9445966 -7.328593 0 2.0e-06 13.37008 T C
416237 cg27611827 Promoter_Associated chr17:41392647-41393089 N_Shore 0.4520915 -2.2371297 7.299569 0 2.2e-06 13.25156 T C
223649 cg13977158 MDP1 Promoter_Associated chr14:24682402-24682837 S_Shelf -0.6471693 -2.8300122 -7.291831 0 2.2e-06 13.21997 T C
400050 cg26528255 TMEM222 chr1:27648453-27649006 S_Shelf -0.4783113 1.2386822 -7.288201 0 2.2e-06 13.20515 T C
223852 cg13986503 TIRAP;TIRAP;TIRAP;TIRAP Promoter_Associated chr11:126152722-126153400 Island 0.2242128 -3.2566271 7.252478 0 2.5e-06 13.05938 T C
97953 cg05742286 chr12:94533729-94533952 Island -0.4484206 1.8133979 -7.251887 0 2.5e-06 13.05698 T C
86608 cg05025913 PPFIBP2 chr11:7534554-7535727 S_Shelf -0.4459729 2.3504268 -7.232261 0 2.6e-06 12.97694 T C
384946 cg25443512 OpenSea -0.4203863 1.1110204 -7.202822 0 2.9e-06 12.85694 T C
127399 cg07565404 RGPD3 chr2:107082328-107084936 Island -0.3291941 1.0824662 -7.201042 0 2.9e-06 12.84968 T C
167348 cg10162522 KCNH5;KCNH5;KCNH5 chr14:63512022-63512996 Island 0.3136629 -3.6335680 7.182273 0 3.1e-06 12.77322 T C
2015 cg00098451 CLCNKB OpenSea -0.3121355 1.0762238 -7.179866 0 3.1e-06 12.76341 T C
105903 cg06254253 ZNF117;ZNF117 OpenSea -0.4163087 2.1321688 -7.148719 0 3.4e-06 12.63658 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 53.451 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_fh_vs_fz.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
MAD1L1 687 -0.4047985 -0.4246183 0e+00 17.129778 0.0000000
PCDHGB2 259 -0.6478783 -0.7264055 0e+00 16.840794 0.0000000
PCDHGA4 273 -0.6267592 -0.6864615 0e+00 16.824113 0.0000000
PCDHGB1 287 -0.6024984 -0.6429736 0e+00 16.539344 0.0000000
PCDHGA5 247 -0.6674691 -0.7358016 0e+00 16.494615 0.0000000
PCDHGA3 305 -0.5715455 -0.5980831 0e+00 16.037279 0.0000000
PCDHGA2 319 -0.5480257 -0.5825170 0e+00 15.698047 0.0000000
PCDHGB3 230 -0.6777183 -0.7558965 0e+00 15.221964 0.0000000
PCDHGA1 327 -0.5180698 -0.5592886 0e+00 14.579714 0.0000000
PCDHGA6 220 -0.6728357 -0.7728996 0e+00 14.497334 0.0000000
PCDHGA7 205 -0.6914949 -0.8006025 0e+00 14.114695 0.0000000
PCDHGB4 193 -0.6838183 -0.7863828 0e+00 12.954796 0.0000000
PCDHA1 170 -0.9548909 -1.1348792 0e+00 12.397957 0.0000000
PCDHGA8 177 -0.6738167 -0.7706570 0e+00 11.507397 0.0000001
TNXB 543 -0.3452342 -0.3885994 0e+00 11.452909 0.0000001
PCDHA2 158 -0.9323911 -1.1315369 0e+00 11.285769 0.0000001
PCDHGB5 161 -0.7041042 -0.8026784 0e+00 10.658268 0.0000004
PCDHGA9 148 -0.7323906 -0.8418808 0e+00 10.333975 0.0000009
PCDHA3 149 -0.9228955 -1.1396466 0e+00 10.277073 0.0000011
NNAT 49 -1.4085327 -1.5379043 0e+00 9.897051 0.0000025
TBCD 336 -0.5140705 -0.5646352 0e+00 9.839377 0.0000029
PCDHGB6 142 -0.7298022 -0.8157475 0e+00 9.827484 0.0000030
MESTIT1 58 -1.2559719 -1.2771024 0e+00 9.707085 0.0000039
HLA-DQB2 49 -1.5401877 -1.6695128 0e+00 9.345069 0.0000090
MEST 84 -0.8843048 -0.8390285 0e+00 9.288843 0.0000102
INPP5A 373 -0.3984057 -0.3782205 0e+00 9.241312 0.0000114
PCDHA4 138 -0.9033325 -1.1315369 0e+00 9.112431 0.0000154
HOXA5 51 1.4195875 1.5355554 0e+00 9.069588 0.0000170
PEG10 105 -0.9587950 -1.1290351 0e+00 8.714490 0.0000384
SGCE 88 -1.0582525 -1.1652821 0e+00 8.368703 0.0000852
PCDHGA10 131 -0.6803805 -0.7751423 0e+00 8.326168 0.0000940
HOXA3 66 -0.7161904 -0.6948871 0e+00 7.563104 0.0005447
PSMB8 83 0.9989199 0.9266989 0e+00 7.556200 0.0005534
BAT4 73 1.1195135 1.1023336 0e+00 7.427978 0.0007435
PCDHA5 128 -0.7695067 -1.0081195 1e-07 7.181023 0.0013128
C11orf21 36 0.9867676 0.8125879 1e-07 6.901573 0.0024982
KCNQ1 302 -0.3366666 -0.3762434 1e-07 6.868215 0.0026975
PCDHGB7 116 -0.6528062 -0.7160387 1e-07 6.849114 0.0028187
RXRB 90 0.7902212 0.7839932 2e-07 6.810543 0.0030803
TAP1 99 0.8475225 0.8161066 2e-07 6.754883 0.0035013
GAK 163 -0.5682780 -0.4427455 2e-07 6.647398 0.0044843
RASA3 328 -0.3629393 -0.2733073 3e-07 6.522331 0.0059805
MAD2L1BP 28 1.1004844 1.1630972 3e-07 6.494341 0.0063783
PAX6 103 0.7720348 0.7763220 3e-07 6.493973 0.0063834
RPH3AL 139 -0.7039415 -0.6141082 4e-07 6.448692 0.0070846
GATA2 47 1.2011777 1.3748486 4e-07 6.420248 0.0075637
EN1 42 1.0043132 1.0306277 4e-07 6.405289 0.0078284
KIAA1949 101 0.9336201 1.0427601 4e-07 6.380092 0.0082956
BANP 169 -0.5186132 -0.5275141 5e-07 6.340435 0.0090883
BRD2 167 0.7227115 0.6300217 6e-07 6.204034 0.0124412 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
1487 alpha-linolenic (omega3) and linoleic (omega6) acid metabolism 12 0.0002515 0.6101359 0.0029410
1488 alpha-linolenic acid (ALA) metabolism 12 0.0002515 0.6101359 0.0029410
56 Activation of the phototransduction cascade 11 0.0005113 -0.6048874 0.0049432
1338 TFAP2 (AP-2) family regulates transcription of growth factors and their receptors 12 0.0004580 0.5840480 0.0045146
436 Folding of actin by CCT/TriC 10 0.0020751 0.5622035 0.0168447
314 Digestion and absorption 24 0.0000659 -0.4704254 0.0011635
417 FGFRL1 modulation of FGFR1 signaling 13 0.0056982 0.4427494 0.0389637
113 Base-Excision Repair, AP Site Formation 18 0.0013193 0.4371534 0.0112510
1481 Xenobiotics 23 0.0002967 -0.4357055 0.0033361
736 Mitochondrial protein import 48 0.0000002 0.4318790 0.0000136
1201 Serotonin receptors 11 0.0181014 0.4114753 0.1025295
362 EPHA-mediated growth cone collapse 15 0.0058947 -0.4105471 0.0399469
29 Acetylcholine Neurotransmitter Release Cycle 16 0.0046224 0.4088726 0.0326698
849 Other interleukin signaling 22 0.0010808 0.4024583 0.0093218
431 Fatty acids 15 0.0079983 -0.3954254 0.0521090
877 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation 12 0.0177538 -0.3951636 0.1013165
313 Digestion 19 0.0030636 -0.3923287 0.0229094
967 Pyrimidine salvage 10 0.0335798 0.3880146 0.1554091
1148 SARS-CoV-2 modulates host translation machinery 45 0.0000077 0.3852663 0.0002321
623 Interleukin-2 signaling 10 0.0359831 0.3829096 0.1635925 
#mitch_report(mres,outfile="gmeawg_mitch_fh_vs_fz.html",overwrite=FALSE)
# Promoter
dm <- fh_vs_fz$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
144399 SMUG1 -7.702697
60057 LCMT1;LCMT1 7.578188
269279 EXPH5 7.436941
43373 YWHAQ 7.392156
416237 7.299569
223649 MDP1 -7.291831
223852 TIRAP;TIRAP;TIRAP;TIRAP 7.252478
342850 SLC12A2;FLJ33630 7.087737
213394 ZNF395;ZNF395 7.066881
398704 TRIM59 7.030297
325586 ATOX1;ATOX1 7.018640
42036 USP5;USP5;CDCA3 6.980545
222351 HIST3H2BB;HIST3H2A;HIST3H2A 6.931982
170816 TMED5;TMED5;TMED5;CCDC18;TMED5;TMED5 6.905321
142728 ABCB9;OGFOD2 6.861415
315340 MUTYH;TOE1;MUTYH;TOE1;MUTYH;MUTYH;MUTYH;MUTYH;MUTYH;MUTYH 6.844968
308736 6.837417
30893 RAP2B 6.810606
412852 CIAO1;CIAO1;TMEM127 6.785565
316219 RAD54L;RAD54L;RAD54L;RAD54L 6.784765
43213 TBL3 6.782186
226146 MAML2 6.760236
294106 DPH2;DPH2 -6.715046
173100 VRK1;VRK1 6.668439
158043 CNOT6 6.665509
265286 PRR7 6.649516
254367 ZFYVE27;ZFYVE27;ZFYVE27 6.644709
210945 DVL2;DVL2 6.626004
337059 DDX46 6.597024
54552 RAET1K 6.569319
176751 KIFC1;KIFC1 6.530728
211069 CLIP4 6.513141
407591 USP36 6.493206
38906 KCTD5 6.472494
217936 KDM6B 6.469878
374338 B4GALT5 6.455784
275515 FUT11 6.450765
71387 PPP2R5E 6.442149
100564 HSPB6;C19orf55 6.440400
150336 CHRNE;C17orf107 6.435352
139955 CD79B;CD79B;CD79B;CD79B;CD79B;CD79B 6.431935
231867 UGCG 6.430724
405265 RIC8A;BET1L;BET1L 6.398601
378399 TRAPPC4;TRAPPC4;RPS25 -6.395100
253709 HDAC4 6.380108
314721 C1orf198;C1orf198 6.372836
75482 HERPUD1;HERPUD1;HERPUD1;HERPUD1;HERPUD1;HERPUD1 6.350972
333107 ARL4C 6.343180
48905 MGC23284;SNAI3 6.334916
29130 LOC100133991;LOC100133991;C17orf46 6.333588 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 29.804 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res ,file="estill_gmeapr_fh_vs_fz.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
PEG10 61 -1.1437574 -1.1743804 0.0000001 7.162381 0.0007096
SGCE 58 -1.1316356 -1.1652821 0.0000002 6.671048 0.0021994
KIAA1949 67 1.2670395 1.2931479 0.0000004 6.426922 0.0038581
BLCAP 47 1.1475021 1.2486196 0.0000007 6.161519 0.0071079
RAP1GAP2 21 1.8490929 1.9307735 0.0000010 6.020600 0.0098314
MAD2L1BP 23 1.1349329 1.2689108 0.0000012 5.923690 0.0122881
MORG1 28 1.4154555 1.3121565 0.0000013 5.899923 0.0129780
TUBB 27 1.7215284 1.4655107 0.0000013 5.882297 0.0135143
LY6G5C 34 1.2824938 1.3045427 0.0000013 5.880067 0.0135825
B3GALT4 50 1.3066101 1.3541604 0.0000019 5.711102 0.0200403
TAPBP 72 1.0328458 1.1198867 0.0000021 5.680209 0.0215157
BAT3 53 1.1708407 1.2928883 0.0000031 5.511440 0.0317309
PSMB9 49 1.0830821 1.0181746 0.0000032 5.496817 0.0328143
BAT4 40 1.2829625 1.2912902 0.0000032 5.495579 0.0329047
CSNK2B 40 1.2829625 1.2912902 0.0000032 5.495579 0.0329047
PRRT1 20 -1.8413417 -2.0582686 0.0000038 5.418540 0.0392838
PSMB8 46 1.2297116 1.2176871 0.0000039 5.413864 0.0397051
ARAP1 18 1.5532794 1.4666978 0.0000076 5.117510 0.0785522
FUCA1 18 1.2693273 1.0847057 0.0000076 5.117510 0.0785522
HNRNPF 35 0.9589217 0.8547382 0.0000087 5.059757 0.0897071
DOM3Z 49 0.9694999 1.0162512 0.0000136 4.866920 0.1398368
STK19 49 0.9694999 1.0162512 0.0000136 4.866920 0.1398368
ESRRA 17 1.6119685 1.5313913 0.0000153 4.816480 0.1570282
TAP1 52 1.0088432 0.9620331 0.0000168 4.773434 0.1733732
HNRNPUL1 24 1.4959618 1.7721764 0.0000201 4.695803 0.2072860
RGL2 56 0.9995613 0.8738350 0.0000203 4.693498 0.2083690
TCF19 30 1.2931736 1.5203483 0.0000237 4.625861 0.2434601
CCHCR1 29 1.3349288 1.5811897 0.0000243 4.614859 0.2496823
FAM50B 29 -0.9806571 -0.9631306 0.0000243 4.614859 0.2496823
SIPA1 19 0.9759117 0.8567926 0.0000267 4.573442 0.2746124
GNB2L1 24 1.0778529 1.0060784 0.0000302 4.520569 0.3101348
HOXA4 16 -1.0718966 -1.0550618 0.0000305 4.515450 0.3137817
SNORD95 21 1.0071370 0.9740244 0.0000315 4.502086 0.3235559
DLG4 22 1.3013356 0.9679473 0.0000334 4.476532 0.3431320
HDAC4 37 0.9329145 1.0392172 0.0000514 4.289192 0.5281517
HDAC11 18 1.3615935 1.5408740 0.0000534 4.272412 0.5489044
HCP5 18 1.2146861 1.2591792 0.0000534 4.272412 0.5489044
ZNF335 15 1.9559674 1.9011872 0.0000610 4.214420 0.6271973
NAP1L5 15 -1.4041956 -1.3406196 0.0000610 4.214420 0.6271973
DNAJC24 15 -1.7531206 -1.6504445 0.0000610 4.214420 0.6271973
DCDC1 15 -1.7531206 -1.6504445 0.0000610 4.214420 0.6271973
KATNB1 15 1.6786841 1.5258200 0.0000610 4.214420 0.6271973
PLD6 16 1.1202953 1.1492968 0.0000610 4.214420 0.6271973
RDBP 26 1.1883702 1.2358964 0.0000702 4.153390 0.7214066
SKIV2L 26 1.1883702 1.2358964 0.0000702 4.153390 0.7214066
BAD 24 1.4694543 1.7721811 0.0000763 4.117510 0.7833862
LOC100131691 31 1.1527728 0.7456714 0.0000778 4.108927 0.7989436
RUFY1 22 0.9134556 1.0116210 0.0000987 4.005660 1.0000000
NEAT1 18 2.6650181 2.4949201 0.0001068 3.971382 1.0000000
SDCCAG1 14 -1.7784781 -1.5306406 0.0001221 3.913390 1.0000000 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1168 alpha-linolenic (omega3) and linoleic (omega6) acid metabolism 10 0.0007005 0.6187421 0.0596395
1169 alpha-linolenic acid (ALA) metabolism 10 0.0007005 0.6187421 0.0596395
84 Binding and Uptake of Ligands by Scavenger Receptors 10 0.0058245 0.5034359 0.1936708
1 A tetrasaccharide linker sequence is required for GAG synthesis 10 0.0129489 0.4537319 0.2230072
221 Degradation of cysteine and homocysteine 10 0.0135188 0.4509269 0.2238107
1166 Zinc transporters 11 0.0122125 -0.4362524 0.2230072
130 Cell-cell junction organization 12 0.0090005 -0.4353784 0.2230072
1077 Termination of O-glycan biosynthesis 10 0.0220388 0.4180530 0.2520753
1026 Sulfur amino acid metabolism 17 0.0042130 0.4008467 0.1643555
418 Heparan sulfate/heparin (HS-GAG) metabolism 22 0.0013970 0.3935036 0.0925154
755 RHO GTPases Activate NADPH Oxidases 14 0.0156445 0.3730459 0.2383938
158 Collagen biosynthesis and modifying enzymes 13 0.0267183 0.3548469 0.2595881
267 ECM proteoglycans 11 0.0428472 0.3525794 0.3412963
627 Nicotinamide salvaging 10 0.0606940 -0.3424828 0.4134126
311 FOXO-mediated transcription of cell cycle genes 12 0.0406523 -0.3412290 0.3296430
466 Interleukin-10 signaling 13 0.0345810 0.3384541 0.3008797
649 Nucleotide salvage 18 0.0130672 0.3378825 0.2230072
795 RNA Polymerase III Chain Elongation 17 0.0198230 0.3263403 0.2411121
673 PKA-mediated phosphorylation of CREB 11 0.0633345 -0.3232735 0.4153309
228 Detoxification of Reactive Oxygen Species 22 0.0109535 0.3133497 0.2230072 
#mitch_report(mres,outfile="gmeapr_mitch_fh_vs_fz.html",overwrite=FALSE)
rm(fh_vs_fz)

nat vs fx

dm <- nat_vs_fx$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
321265 cg20757019 Unclassified chr2:95872891-95873548 Island -1.1542534 -4.280613 -23.23637 0 0 94.18962 T C
132599 cg07897831 CASKIN2;TSEN54 Unclassified chr17:73511016-73513176 Island -0.8721412 -4.455889 -21.53238 0 0 87.04881 T C
26062 cg01447112 Unclassified_Cell_type_specific chr7:6703503-6704075 Island -1.0002478 -3.896946 -21.53224 0 0 87.04823 T C
234473 cg14572967 CD72 Promoter_Associated chr9:35616980-35617324 Island -1.0414923 -4.824333 -21.18933 0 0 85.56578 T C
286730 cg18233405 TSPYL5;TSPYL5 Promoter_Associated chr8:98289604-98290404 Island -0.9083285 -4.751098 -20.87168 0 0 84.17874 T C
51218 cg02916102 CYP11A1;CYP11A1;CYP11A1 Unclassified_Cell_type_specific chr15:74658038-74658574 Island -1.0045920 -4.570302 -20.03054 0 0 80.44118 T C
138436 cg08260549 XPO7;XPO7 Promoter_Associated chr8:21776842-21777942 Island -0.9965532 -4.331345 -19.92419 0 0 79.96188 T C
63905 cg03655371 chr5:134827285-134827644 Island -0.8888073 -4.175950 -19.66463 0 0 78.78578 T C
268273 cg16905586 GMPPB;GMPPB;GMPPB;GMPPB Promoter_Associated chr3:49760863-49761895 Island -0.6825232 -3.665415 -19.64924 0 0 78.71572 T C
34194 cg01931797 KCTD21;USP35 Promoter_Associated chr11:77899564-77899990 Island -1.0190148 -4.651235 -19.51724 0 0 78.11389 T C
291292 cg18555811 HES1 Unclassified chr3:193854575-193856015 N_Shore -1.0441527 -4.605924 -19.45339 0 0 77.82190 T C
267523 cg16849041 DOCK5;DOCK5 chr8:25041795-25042820 Island -1.0473607 -4.636067 -19.43416 0 0 77.73387 T C
312054 cg20064047 ASH1L;LOC645676 Promoter_Associated chr1:155531914-155533280 Island -1.0488456 -4.836609 -19.33641 0 0 77.28555 T C
196471 cg12159575 UHRF1;UHRF1 Promoter_Associated chr19:4909262-4910256 S_Shore -1.0312195 -4.734009 -19.31461 0 0 77.18540 T C
395222 cg26206990 APH1B;APH1B chr15:63569296-63570100 Island -0.8972474 -3.196506 -19.30547 0 0 77.14337 T C
364043 cg23963136 CD320;CD320 Promoter_Associated chr19:8372597-8373302 Island -1.1304698 -4.933567 -19.12396 0 0 76.30677 T C
195450 cg12089543 C22orf40 Unclassified chr22:46645764-46646957 Island -0.8221062 -4.667655 -19.05652 0 0 75.99478 T C
313948 cg20213228 chr20:61806254-61810867 Island -1.1109881 -4.855896 -18.99514 0 0 75.71031 T C
235315 cg14618681 E2F1 Promoter_Associated chr20:32273557-32274505 Island -1.0444915 -4.697211 -18.95255 0 0 75.51261 T C
95181 cg05563672 TMPRSS2;TMPRSS2;TMPRSS2 chr21:42878751-42880674 Island -0.7579948 -3.980350 -18.74589 0 0 74.54993 T C
359726 cg23649004 KCNJ4 chr22:38850766-38851285 S_Shore -0.9524635 -4.173596 -18.72030 0 0 74.43030 T C
342396 cg22394521 DIDO1;DIDO1;C20orf11;DIDO1 Promoter_Associated chr20:61568678-61569916 Island -0.8828815 -4.512412 -18.67790 0 0 74.23195 T C
107155 cg06347499 SLC25A33 Promoter_Associated chr1:9599350-9600444 Island -1.0157752 -4.469872 -18.63223 0 0 74.01798 T C
66567 cg03817939 FAM176A;FAM176A chr2:75787717-75788312 Island -0.9517871 -4.382623 -18.59270 0 0 73.83261 T C
358320 cg23543263 FGF9 Promoter_Associated chr13:22243259-22245362 Island -1.0272112 -4.316506 -18.51003 0 0 73.44416 T C
110655 cg06571075 MACROD2 chr20:13975768-13976287 Island -1.0312770 -4.791716 -18.40980 0 0 72.97202 T C
207083 cg12950624 RTN2;RTN2;RTN2;RTN2 Unclassified chr19:45999761-46000210 Island -0.9961217 -3.774533 -18.40306 0 0 72.94023 T C
372380 cg24543097 RBCK1;RBCK1 Promoter_Associated chr20:388472-389342 Island -0.8432685 -4.144888 -18.27986 0 0 72.35788 T C
80305 cg04645421 Unclassified chr5:108063600-108064072 Island -0.6038165 -4.143363 -18.23755 0 0 72.15743 T C
398413 cg26415547 IRAK3;IRAK3;IRAK3;IRAK3 Promoter_Associated_Cell_type_specific chr12:66582695-66583345 Island -0.8043382 -4.781634 -18.19148 0 0 71.93889 T C
136031 cg08115069 COX6B2;FAM71E2 Unclassified chr19:55864130-55864379 S_Shore -0.7901566 -4.268687 -18.12015 0 0 71.59995 T C
116889 cg06931446 ARHGEF18 Unclassified chr19:7459779-7460376 Island -0.8568490 -3.990599 -18.11901 0 0 71.59452 T C
179618 cg10992925 SEMA3F Unclassified chr3:50191971-50193130 Island -0.7063194 -3.375737 -18.05096 0 0 71.27051 T C
221706 cg13871588 MEA1;KLHDC3 Promoter_Associated chr6:42981408-42982077 Island -0.9104098 -4.914230 -17.96399 0 0 70.85557 T C
374812 cg24713789 AGPAT3 Promoter_Associated OpenSea -0.8415852 -4.337121 -17.82546 0 0 70.19247 T C
176371 cg10769393 ZNF554 Promoter_Associated chr19:2819630-2820295 Island -1.0591294 -3.956990 -17.72384 0 0 69.70441 T C
323682 cg20958497 Promoter_Associated chr19:18058664-18059218 Island -0.8387456 -4.808823 -17.53207 0 0 68.77969 T C
356507 cg23411876 LOC100134713;NDUFB2 Promoter_Associated chr7:140396414-140397357 Island -0.8780381 -3.432529 -17.45679 0 0 68.41538 T C
260863 cg16415121 ORC3L;ORC3L;RARS2 Promoter_Associated chr6:88299620-88299945 Island -0.9158515 -4.639066 -17.39421 0 0 68.11194 T C
32034 cg01805784 PRR7;PRR7 Promoter_Associated chr5:176873349-176874737 Island -0.8840711 -4.245490 -17.36815 0 0 67.98540 T C
255870 cg16080015 RBAK Promoter_Associated chr7:5085411-5086342 Island -0.8506736 -4.458150 -17.34777 0 0 67.88639 T C
333237 cg21660960 SLC40A1 chr2:190445459-190445983 Island -0.9348836 -3.846481 -17.34436 0 0 67.86983 T C
338499 cg22083815 CCDC28B Promoter_Associated chr1:32666231-32666460 Island -1.0201641 -5.076298 -17.23432 0 0 67.33425 T C
283544 cg18023558 WDR1;WDR1;WDR1;WDR1 Promoter_Associated chr4:10117575-10118952 Island -0.7826295 -4.719027 -17.18113 0 0 67.07484 T C
96919 cg05671241 Promoter_Associated_Cell_type_specific chr3:126373571-126374142 Island -0.6724936 -3.760453 -17.17332 0 0 67.03670 T C
346062 cg22686066 TAF4 Promoter_Associated chr20:60640721-60641805 Island -0.6354485 -3.679035 -17.16932 0 0 67.01717 T C
388254 cg25692259 FARSB Promoter_Associated chr2:223520516-223520893 Island -0.6045603 -3.607936 -17.16356 0 0 66.98906 T C
381817 cg25214684 AKIRIN1;AKIRIN1 Promoter_Associated chr1:39456655-39457271 Island -0.8331174 -5.042280 -17.13187 0 0 66.83422 T C
11885 cg00645897 RAD54L;RAD54L;RAD54L Promoter_Associated OpenSea -1.0284646 -5.223037 -17.02123 0 0 66.29263 T C
169177 cg10277546 DONSON;DONSON Promoter_Associated chr21:34960388-34961252 Island -0.8540001 -4.658442 -16.98278 0 0 66.10405 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 56.726 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_nat_vs_fx.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
TNXB 543 -2.3125210 -2.6616132 0 52.496075 0.00e+00
COL11A2 226 -2.4248425 -2.6505270 0 21.098335 0.00e+00
GNAS 190 -2.5946970 -2.3588484 0 19.521131 0.00e+00
PRDM16 608 -1.1295901 -1.1446533 0 19.211717 0.00e+00
KCNQ1 302 -1.5748394 -1.5993948 0 17.817201 0.00e+00
GALNT9 234 -1.7749400 -2.0872511 0 15.971900 0.00e+00
PCDHA1 170 -1.6465328 -1.5290879 0 15.844956 0.00e+00
TP73 123 -2.9457039 -3.3042467 0 15.173052 0.00e+00
PCDHA2 158 -1.6612798 -1.5485573 0 14.793255 0.00e+00
PCDHA3 149 -1.6824100 -1.5677566 0 14.267764 0.00e+00
SGCE 88 -2.9827943 -2.9750401 0 14.063804 0.00e+00
HCCA2 245 -1.5426582 -1.5057488 0 13.859506 0.00e+00
CACNA1H 159 -1.9530850 -1.8992410 0 13.077184 0.00e+00
OBSCN 127 -2.4308397 -2.5761160 0 12.929616 0.00e+00
PCDHA4 138 -1.6244053 -1.5623260 0 12.700486 0.00e+00
BAHCC1 109 -2.3795374 -2.4041415 0 12.613076 0.00e+00
MAD1L1 687 -0.8414090 -0.9138047 0 12.300223 0.00e+00
GNASAS 88 -3.5591825 -3.1886204 0 12.234719 0.00e+00
PEG10 105 -2.4611498 -2.6309536 0 12.187292 0.00e+00
MEGF6 133 -2.1935285 -2.2844831 0 12.163304 0.00e+00
GPR123 94 -2.6132890 -2.8454282 0 11.529912 1.00e-07
VENTX 45 -3.0667883 -3.2224911 0 11.300837 1.00e-07
NNAT 49 -2.6370520 -2.5808923 0 11.209140 1.00e-07
RNF39 86 -2.5075239 -2.6199979 0 11.199672 1.00e-07
SLC9A3 102 -2.2767643 -2.6096991 0 11.192386 1.00e-07
PTPRN2 1197 -0.5268966 -0.5225712 0 11.101660 2.00e-07
PCDHA5 128 -1.5531275 -1.5395340 0 11.096371 2.00e-07
INS-IGF2 138 -1.9010816 -1.8638106 0 11.021695 2.00e-07
BAI1 82 -2.8154965 -2.9946633 0 10.828647 3.00e-07
BLCAP 119 -1.8698230 -2.0984339 0 10.704125 4.00e-07
HDAC4 405 -0.9351213 -0.9595336 0 10.626666 5.00e-07
BRSK2 103 -2.3547036 -2.7319260 0 10.563824 5.00e-07
CAMTA1 237 -1.4232906 -1.3456976 0 10.562953 5.00e-07
SEPT9 160 -1.6521000 -2.1159768 0 10.433274 7.00e-07
PLEC1 145 -2.0587499 -2.3549793 0 10.404282 8.00e-07
PCDHA6 120 -1.5451986 -1.5395340 0 10.243254 1.10e-06
ZBTB12 76 -2.9273793 -3.0796604 0 10.125573 1.50e-06
H19 61 -4.3640677 -4.6820096 0 10.117114 1.50e-06
LOC645323 83 -2.1412125 -2.2533372 0 9.537445 5.80e-06
VAX1 39 -3.1899282 -3.2664669 0 9.494657 6.40e-06
ASCL2 49 -3.2180736 -3.9166648 0 9.490475 6.40e-06
PLCH2 64 -3.4780209 -3.7658261 0 9.385272 8.20e-06
SORCS2 186 -1.3250308 -1.2304313 0 9.254031 1.11e-05
CASZ1 169 -1.5095386 -1.3525348 0 9.210997 1.22e-05
PCDHA7 109 -1.4851688 -1.4232990 0 9.092301 1.61e-05
MEST 84 -2.3637004 -1.9955502 0 9.068194 1.70e-05
PRRT1 78 -1.9744913 -2.2742287 0 8.978277 2.09e-05
PRR5-ARHGAP8 45 -3.3173487 -3.4342949 0 8.962924 2.17e-05
ZIC1 46 -2.0333714 -1.9357867 0 8.941757 2.28e-05
GRIN2D 39 -2.6879469 -2.4319839 0 8.788832 3.24e-05 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
395 Expression and translocation of olfactory receptors 311 0.0000000 0.6586791 0.0000000
840 Olfactory Signaling Pathway 318 0.0000000 0.6426229 0.0000000
1416 Transcriptional regulation of testis differentiation 12 0.0002608 -0.6086146 0.0081446
1490 eNOS activation 11 0.0006735 -0.5919395 0.0170390
276 Defective B3GAT3 causes JDSSDHD 17 0.0000277 -0.5870372 0.0015015
277 Defective B4GALT7 causes EDS, progeroid type 17 0.0000528 -0.5662156 0.0026715
1493 mRNA Editing 10 0.0022608 0.5575648 0.0349437
136 CD28 dependent Vav1 pathway 11 0.0023804 0.5289323 0.0357764
274 Defective B3GALT6 causes EDSP2 and SEMDJL1 17 0.0001758 -0.5254103 0.0060662
712 Metabolism of nitric oxide: NOS3 activation and regulation 15 0.0007102 -0.5047887 0.0176740
909 Phosphorylation of CD3 and TCR zeta chains 20 0.0001096 0.4995259 0.0043784
1429 Translocation of ZAP-70 to Immunological synapse 17 0.0003629 0.4994069 0.0100301
658 LGI-ADAM interactions 14 0.0015220 -0.4892984 0.0268586
562 Hormone ligand-binding receptors 12 0.0038167 0.4822250 0.0454733
445 Formation of apoptosome 10 0.0088410 -0.4780603 0.0667696
1115 Regulation of the apoptosome activity 10 0.0088410 -0.4780603 0.0667696
115 Beta defensins 28 0.0000129 0.4761206 0.0007878
509 Glucuronidation 19 0.0003835 0.4704918 0.0103959
1508 p75NTR recruits signalling complexes 12 0.0050974 -0.4668740 0.0511203
1 A tetrasaccharide linker sequence is required for GAG synthesis 23 0.0001203 -0.4630976 0.0046835 
#mitch_report(mres,outfile="gmeawg_mitch_nat_vs_fx.html",overwrite=FALSE)
# Promoter
dm <- nat_vs_fx$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
234473 CD72 -21.18933
286730 TSPYL5;TSPYL5 -20.87168
138436 XPO7;XPO7 -19.92419
268273 GMPPB;GMPPB;GMPPB;GMPPB -19.64924
34194 KCTD21;USP35 -19.51724
312054 ASH1L;LOC645676 -19.33641
196471 UHRF1;UHRF1 -19.31461
364043 CD320;CD320 -19.12396
235315 E2F1 -18.95255
342396 DIDO1;DIDO1;C20orf11;DIDO1 -18.67790
107155 SLC25A33 -18.63223
358320 FGF9 -18.51003
372380 RBCK1;RBCK1 -18.27986
398413 IRAK3;IRAK3;IRAK3;IRAK3 -18.19148
221706 MEA1;KLHDC3 -17.96399
374812 AGPAT3 -17.82546
176371 ZNF554 -17.72384
323682 -17.53207
356507 LOC100134713;NDUFB2 -17.45679
260863 ORC3L;ORC3L;RARS2 -17.39421
32034 PRR7;PRR7 -17.36815
255870 RBAK -17.34777
338499 CCDC28B -17.23432
283544 WDR1;WDR1;WDR1;WDR1 -17.18113
96919 -17.17332
346062 TAF4 -17.16932
388254 FARSB -17.16356
381817 AKIRIN1;AKIRIN1 -17.13187
11885 RAD54L;RAD54L;RAD54L -17.02123
169177 DONSON;DONSON -16.98278
55372 HTR7P;HEBP1 -16.96035
121274 ITGAV;ITGAV -16.86830
389530 GYS1;GYS1;RUVBL2;GYS1 -16.82422
336088 RNF216L;RNF216L;RNF216L -16.82130
217916 RANBP3;RANBP3;RANBP3 -16.76088
239889 QARS -16.74673
55136 -16.68387
93032 MYO9A;SENP8;SENP8 -16.67402
114200 CREM;CREM;CREM;CREM;CREM;CREM -16.58711
304268 C14orf43 -16.55010
54325 G3BP2;G3BP2;G3BP2;G3BP2;G3BP2 -16.51058
252955 PTTG1IP -16.47554
322086 MCF2L2 -16.43788
389806 ZNF589 -16.42485
304786 RPL23AP82;RABL2B;RABL2B;RABL2B;RPL23AP82;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B -16.40512
319883 PSTPIP2;PSTPIP2 -16.29345
40243 TCFL5 -16.26998
416377 PPAP2A;RNF138P1;PPAP2A -16.25786
228488 RALGAPB -16.18634
395530 BRPF1;BRPF1 -16.17907 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 32.88 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res ,file="estill_gmeapr_nat_vs_fx.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
PEG10 61 -3.863865 -4.067382 0.00e+00 10.878664 0.0000001
SGCE 58 -3.775562 -3.939101 0.00e+00 10.375684 0.0000004
FAM50B 29 -4.852267 -5.279330 0.00e+00 7.951719 0.0001152
RASA3 34 -3.128413 -2.863451 0.00e+00 7.892597 0.0001320
MGC23284 27 -4.439106 -4.234569 1.00e-07 7.127810 0.0007681
RPP21 35 -2.781018 -2.962905 2.00e-07 6.728109 0.0019278
HDAC4 37 -2.436940 -1.826279 3.00e-07 6.501983 0.0032445
PTEN 53 -2.766481 -2.397587 4.00e-07 6.406330 0.0040435
FAM134C 22 -4.794642 -4.338413 5.00e-07 6.321630 0.0049138
TUBG1 22 -4.794642 -4.338413 5.00e-07 6.321630 0.0049138
SNORD48 23 -3.200328 -2.835571 5.00e-07 6.321630 0.0049138
ZBTB9 35 -2.501717 -2.249394 6.00e-07 6.238114 0.0059540
VARS2 40 -2.017411 -1.440234 6.00e-07 6.233466 0.0060175
NFKB2 24 -3.892679 -3.958829 6.00e-07 6.224720 0.0061393
KILLIN 54 -2.682164 -2.396352 6.00e-07 6.208586 0.0063710
TRIM27 53 -1.952970 -2.298284 7.00e-07 6.166172 0.0070239
PCNA 22 -3.986260 -3.808758 1.00e-06 6.020600 0.0098200
L3MBTL 22 -3.702175 -2.939137 1.00e-06 6.020600 0.0098200
ST7OT4 22 -3.339745 -3.201743 1.00e-06 6.020600 0.0098200
ST7OT1 22 -3.339745 -3.201743 1.00e-06 6.020600 0.0098200
ST7 22 -3.339745 -3.201743 1.00e-06 6.020600 0.0098200
ZBTB12 34 -3.249816 -3.060890 1.50e-06 5.823164 0.0154645
DDAH2 39 -2.627727 -3.036743 1.90e-06 5.721552 0.0195392
SKIV2L2 20 -3.780143 -3.588999 1.90e-06 5.719570 0.0196266
DHX29 20 -3.780143 -3.588999 1.90e-06 5.719570 0.0196266
CYP51A1 20 -3.056442 -3.152682 1.90e-06 5.719570 0.0196266
WRB 21 -1.983172 -1.452839 2.90e-06 5.543479 0.0294313
MGMT 19 -3.518832 -2.903853 3.80e-06 5.418540 0.0392380
DNAJC30 19 -4.018711 -3.897512 3.80e-06 5.418540 0.0392380
WBSCR22 19 -4.018711 -3.897512 3.80e-06 5.418540 0.0392380
MOBKL2A 19 -4.256853 -3.699106 3.80e-06 5.418540 0.0392380
C14orf21 19 -3.196772 -3.121999 3.80e-06 5.418540 0.0392380
DHRS1 19 -3.196772 -3.121999 3.80e-06 5.418540 0.0392380
DAXX 38 -2.223381 -2.590220 4.50e-06 5.342431 0.0467264
CCDC59 21 -2.552862 -1.981215 4.80e-06 5.321630 0.0490141
C12orf26 21 -2.552862 -1.981215 4.80e-06 5.321630 0.0490141
TCF19 30 -3.027003 -3.172336 5.10e-06 5.288646 0.0528713
C7orf50 25 -3.179345 -3.185428 5.20e-06 5.280237 0.0538998
CCHCR1 29 -3.157484 -3.207180 5.50e-06 5.257699 0.0567653
FLOT1 68 -2.294863 -2.256312 5.70e-06 5.243539 0.0586409
MIR548N 38 -2.493943 -2.167847 6.60e-06 5.180443 0.0678039
MTIF3 22 -3.831177 -3.276042 6.70e-06 5.175502 0.0685730
C6orf48 42 -2.087671 -2.099175 7.50e-06 5.123567 0.0772761
PITPNC1 18 -2.922945 -1.770851 7.60e-06 5.117510 0.0783539
CENPT 29 -3.492049 -3.533389 8.80e-06 5.053725 0.0907409
RAB1B 58 -2.365782 -3.293321 9.50e-06 5.023024 0.0973782
ACTR3C 20 -3.519671 -3.588760 9.50e-06 5.020600 0.0979137
LRRC61 20 -3.519671 -3.588760 9.50e-06 5.020600 0.0979137
C19orf47 19 -4.035601 -3.701569 1.14e-05 4.941419 0.1174736
PLD3 19 -4.035601 -3.701569 1.14e-05 4.941419 0.1174736 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1077 Termination of O-glycan biosynthesis 10 0.0001261 0.7000679 0.1044428
313 FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes 14 0.0048405 -0.4349590 0.4438338
553 Methylation 10 0.0179655 -0.4321848 0.5122146
30 Activation of G protein gated Potassium channels 11 0.0294981 0.3790879 0.5122146
341 G protein gated Potassium channels 11 0.0294981 0.3790879 0.5122146
443 Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 11 0.0294981 0.3790879 0.5122146
677 PRC2 methylates histones and DNA 11 0.0331602 -0.3709694 0.5122146
340 G beta:gamma signalling through PLC beta 12 0.0291450 0.3637592 0.5122146
719 Presynaptic function of Kainate receptors 12 0.0291450 0.3637592 0.5122146
1166 Zinc transporters 11 0.0374824 -0.3623215 0.5122146
1159 Vitamin B5 (pantothenate) metabolism 11 0.0375940 0.3621097 0.5122146
972 Signaling by Hippo 11 0.0450436 -0.3490496 0.5122146
1027 Suppression of phagosomal maturation 12 0.0377171 -0.3464874 0.5122146
337 G beta:gamma signalling through BTK 10 0.0581318 0.3460643 0.5361027
142 Cholesterol biosynthesis 20 0.0081768 -0.3417031 0.4892200
1056 TNFR1-induced proapoptotic signaling 12 0.0416686 -0.3396353 0.5122146
1085 Thromboxane signalling through TP receptor 13 0.0359236 0.3360941 0.5122146
607 Negative regulation of FGFR1 signaling 17 0.0180561 -0.3313223 0.5122146
608 Negative regulation of FGFR2 signaling 17 0.0180561 -0.3313223 0.5122146
609 Negative regulation of FGFR3 signaling 17 0.0180561 -0.3313223 0.5122146 
#mitch_report(mres,outfile="gmeapr_mitch_nat_vs_fx.html",overwrite=FALSE)
rm(nat_vs_fx)

nat vs fz

dm <- nat_vs_fz$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
321265 cg20757019 Unclassified chr2:95872891-95873548 Island -1.0912788 -4.055613 -18.75632 0 0 60.55961 T C
115170 cg06834912 FOXF1 chr16:86549069-86550512 N_Shore -3.0695412 -4.131474 -18.43307 0 0 59.45493 T C
51218 cg02916102 CYP11A1;CYP11A1;CYP11A1 Unclassified_Cell_type_specific chr15:74658038-74658574 Island -1.0306961 -4.411861 -18.09825 0 0 58.29625 T C
234473 cg14572967 CD72 Promoter_Associated chr9:35616980-35617324 Island -1.0445143 -4.649812 -17.81013 0 0 57.28725 T C
107155 cg06347499 SLC25A33 Promoter_Associated chr1:9599350-9600444 Island -1.0848915 -4.327655 -17.30676 0 0 55.49783 T C
267523 cg16849041 DOCK5;DOCK5 chr8:25041795-25042820 Island -1.1207092 -4.494514 -17.28354 0 0 55.41446 T C
26062 cg01447112 Unclassified_Cell_type_specific chr7:6703503-6704075 Island -0.9817009 -3.721752 -16.97521 0 0 54.30055 T C
132599 cg07897831 CASKIN2;TSEN54 Unclassified chr17:73511016-73513176 Island -0.8559384 -4.302864 -16.92677 0 0 54.12437 T C
286730 cg18233405 TSPYL5;TSPYL5 Promoter_Associated chr8:98289604-98290404 Island -0.8846823 -4.587352 -16.86416 0 0 53.89617 T C
358320 cg23543263 FGF9 Promoter_Associated chr13:22243259-22245362 Island -1.0784487 -4.168464 -16.82315 0 0 53.74642 T C
63905 cg03655371 chr5:134827285-134827644 Island -0.8646089 -4.016791 -16.74878 0 0 53.47426 T C
34194 cg01931797 KCTD21;USP35 Promoter_Associated chr11:77899564-77899990 Island -1.0282176 -4.484584 -16.54969 0 0 52.74197 T C
291292 cg18555811 HES1 Unclassified chr3:193854575-193856015 N_Shore -1.0619404 -4.441491 -16.50785 0 0 52.58739 T C
312054 cg20064047 ASH1L;LOC645676 Promoter_Associated chr1:155531914-155533280 Island -1.0646644 -4.667459 -16.42457 0 0 52.27898 T C
195450 cg12089543 C22orf40 Unclassified chr22:46645764-46646957 Island -0.8250568 -4.528109 -16.42311 0 0 52.27358 T C
398413 cg26415547 IRAK3;IRAK3;IRAK3;IRAK3 Promoter_Associated_Cell_type_specific chr12:66582695-66583345 Island -0.8055475 -4.647584 -16.29557 0 0 51.79939 T C
333237 cg21660960 SLC40A1 chr2:190445459-190445983 Island -1.0220766 -3.729143 -16.17481 0 0 51.34835 T C
138436 cg08260549 XPO7;XPO7 Promoter_Associated chr8:21776842-21777942 Island -1.0081365 -4.171851 -16.14727 0 0 51.24523 T C
364043 cg23963136 CD320;CD320 Promoter_Associated chr19:8372597-8373302 Island -1.1651024 -4.761942 -16.08581 0 0 51.01466 T C
359726 cg23649004 KCNJ4 chr22:38850766-38851285 S_Shore -0.9106571 -3.993270 -15.98636 0 0 50.64052 T C
313948 cg20213228 chr20:61806254-61810867 Island -1.1443800 -4.680523 -15.84620 0 0 50.11087 T C
190357 cg11755107 C8orf41;C8orf41 Unclassified_Cell_type_specific chr8:33371897-33372526 Island -0.9801968 -4.273302 -15.79346 0 0 49.91090 T C
196471 cg12159575 UHRF1;UHRF1 Promoter_Associated chr19:4909262-4910256 S_Shore -1.0261903 -4.557819 -15.61601 0 0 49.23519 T C
235315 cg14618681 E2F1 Promoter_Associated chr20:32273557-32274505 Island -1.0756689 -4.535594 -15.48926 0 0 48.74986 T C
95181 cg05563672 TMPRSS2;TMPRSS2;TMPRSS2 chr21:42878751-42880674 Island -0.7438152 -3.845832 -15.35730 0 0 48.24229 T C
268273 cg16905586 GMPPB;GMPPB;GMPPB;GMPPB Promoter_Associated chr3:49760863-49761895 Island -0.6164194 -3.519393 -15.33406 0 0 48.15261 T C
11885 cg00645897 RAD54L;RAD54L;RAD54L Promoter_Associated OpenSea -1.0394837 -5.059687 -15.32834 0 0 48.13055 T C
304786 cg19565306 RPL23AP82;RABL2B;RABL2B;RABL2B;RPL23AP82;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B Promoter_Associated_Cell_type_specific chr22:51221772-51222317 Island -0.9861067 -4.741498 -15.29932 0 0 48.01850 T C
110655 cg06571075 MACROD2 chr20:13975768-13976287 Island -1.0371181 -4.618557 -15.29415 0 0 47.99850 T C
80305 cg04645421 Unclassified chr5:108063600-108064072 Island -0.5889769 -4.036276 -15.18032 0 0 47.55775 T C
93032 cg05414026 MYO9A;SENP8;SENP8 Promoter_Associated chr15:72409862-72411002 Island -1.0598069 -4.119708 -15.15397 0 0 47.45547 T C
239889 cg14930269 QARS Promoter_Associated chr3:49141934-49142373 Island -0.7930329 -3.814041 -15.11431 0 0 47.30133 T C
342396 cg22394521 DIDO1;DIDO1;C20orf11;DIDO1 Promoter_Associated chr20:61568678-61569916 Island -0.8520815 -4.351362 -15.06928 0 0 47.12607 T C
395222 cg26206990 APH1B;APH1B chr15:63569296-63570100 Island -0.8775043 -3.037090 -15.02276 0 0 46.94470 T C
55372 cg03157633 HTR7P;HEBP1 Promoter_Associated chr12:13154088-13154866 Island -0.9525789 -4.451798 -14.99003 0 0 46.81694 T C
136031 cg08115069 COX6B2;FAM71E2 Unclassified chr19:55864130-55864379 S_Shore -0.7810529 -4.131527 -14.96039 0 0 46.70111 T C
283544 cg18023558 WDR1;WDR1;WDR1;WDR1 Promoter_Associated chr4:10117575-10118952 Island -0.7817992 -4.584162 -14.94089 0 0 46.62484 T C
323670 cg20957382 KIAA1033 chr12:105501333-105501908 Island -0.7989841 -4.208778 -14.88463 0 0 46.40447 T C
169177 cg10277546 DONSON;DONSON Promoter_Associated chr21:34960388-34961252 Island -0.8773479 -4.525978 -14.85326 0 0 46.28141 T C
207083 cg12950624 RTN2;RTN2;RTN2;RTN2 Unclassified chr19:45999761-46000210 Island -0.9738680 -3.597778 -14.83512 0 0 46.21018 T C
261873 cg16482183 HIST1H1C Promoter_Associated chr6:26056167-26056798 Island -0.9307518 -4.269910 -14.75838 0 0 45.90841 T C
179618 cg10992925 SEMA3F Unclassified chr3:50191971-50193130 Island -0.6602943 -3.232984 -14.73234 0 0 45.80582 T C
96919 cg05671241 Promoter_Associated_Cell_type_specific chr3:126373571-126374142 Island -0.6607736 -3.643226 -14.71827 0 0 45.75037 T C
128610 cg07637658 PPP1R13L;PPP1R13L chr19:45888768-45889465 N_Shore -0.9283439 1.652684 -14.69335 0 0 45.65203 T C
240020 cg14940308 EMX1;EMX1 Unclassified chr2:73143055-73148260 Island -0.8705505 -4.361189 -14.67532 0 0 45.58086 T C
66567 cg03817939 FAM176A;FAM176A chr2:75787717-75788312 Island -0.9299988 -4.209059 -14.61204 0 0 45.33069 T C
338499 cg22083815 CCDC28B Promoter_Associated chr1:32666231-32666460 Island -1.0432887 -4.914043 -14.54160 0 0 45.05157 T C
55136 cg03144494 Promoter_Associated chr17:79314962-79320653 Island -1.0004139 -4.511161 -14.53173 0 0 45.01241 T C
356507 cg23411876 LOC100134713;NDUFB2 Promoter_Associated chr7:140396414-140397357 Island -0.9351864 -3.312479 -14.48469 0 0 44.82559 T C
202957 cg12636108 GPRIN1 Unclassified chr5:176036458-176037557 Island -0.8940254 -4.287522 -14.48459 0 0 44.82516 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 65.602 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_nat_vs_fz.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
TNXB 543 -2.0912615 -2.3011503 0 54.856929 0.00e+00
COL11A2 226 -2.0747094 -2.2572083 0 20.795431 0.00e+00
PCDHA1 170 -1.8393618 -1.8565164 0 20.766033 0.00e+00
GNAS 190 -2.2846799 -1.9729289 0 19.842594 0.00e+00
PRDM16 608 -1.0220034 -1.0014768 0 19.759790 0.00e+00
PCDHA2 158 -1.8389130 -1.8798292 0 19.358230 0.00e+00
KCNQ1 302 -1.4615991 -1.4523478 0 19.221080 0.00e+00
PCDHA3 149 -1.8481519 -1.9023710 0 18.406594 0.00e+00
MAD1L1 687 -0.9160421 -0.8905487 0 16.874547 0.00e+00
PCDHA4 138 -1.7817780 -1.8470383 0 16.623350 0.00e+00
GALNT9 234 -1.5255836 -1.6930553 0 15.216320 0.00e+00
PCDHA5 128 -1.6648384 -1.7059758 0 14.634120 0.00e+00
TP73 123 -2.4947142 -2.8794962 0 14.054060 0.00e+00
SGCE 88 -2.8117324 -2.7647462 0 13.794493 0.00e+00
PCDHA6 120 -1.6237690 -1.6380702 0 13.515196 0.00e+00
PTPRN2 1197 -0.5326231 -0.4788747 0 13.493153 0.00e+00
OBSCN 127 -2.2227541 -2.3968496 0 13.367276 0.00e+00
NNAT 49 -3.0438182 -2.9297468 0 13.170686 0.00e+00
MEGF6 133 -2.0431772 -2.3841546 0 13.012947 0.00e+00
GNASAS 88 -3.1470366 -3.0161990 0 12.811766 0.00e+00
BAHCC1 109 -2.0923945 -1.9704399 0 12.770171 0.00e+00
PEG10 105 -2.3551896 -2.5050398 0 12.535526 0.00e+00
HDAC4 405 -0.9254866 -0.8271085 0 12.119460 0.00e+00
CACNA1H 159 -1.5997891 -1.7047733 0 12.060442 0.00e+00
HCCA2 245 -1.2248714 -1.2629361 0 11.969247 0.00e+00
PCDHA7 109 -1.5273657 -1.5260919 0 11.757464 0.00e+00
BRSK2 103 -2.0549214 -2.4091248 0 10.996061 2.00e-07
CASZ1 169 -1.4824881 -1.5319457 0 10.891489 3.00e-07
GPR123 94 -2.0713363 -2.1781264 0 10.864001 3.00e-07
BAI1 82 -2.4966507 -2.6647315 0 10.553733 6.00e-07
PCDHGB3 230 -0.8779169 -0.6896332 0 10.442811 7.00e-07
RNF39 86 -2.0466722 -2.0644985 0 10.414442 8.00e-07
CAMTA1 237 -1.2162331 -1.1948028 0 10.398607 8.00e-07
PCDHGA5 247 -0.8436642 -0.6710315 0 10.375608 8.00e-07
SLC9A3 102 -1.8467169 -1.9680029 0 10.326193 9.00e-07
PCDHA8 99 -1.5195318 -1.5732472 0 10.309856 1.00e-06
MEST 84 -2.2998866 -1.8738340 0 10.172941 1.30e-06
H19 61 -3.8769626 -4.2133303 0 9.972338 2.10e-06
PRRT1 78 -1.8899062 -2.1793395 0 9.965855 2.20e-06
SEPT9 160 -1.3837350 -1.7744875 0 9.846730 2.80e-06
PLEC1 145 -1.8023484 -2.0895198 0 9.822600 3.00e-06
BLCAP 119 -1.6958824 -1.7941003 0 9.688724 4.10e-06
INS-IGF2 138 -1.4585811 -1.6248169 0 9.655988 4.40e-06
PCDHGA6 220 -0.8716348 -0.6606173 0 9.570151 5.40e-06
PLCH2 64 -3.3249482 -3.3248588 0 9.441140 7.20e-06
VENTX 45 -2.3870823 -2.7621181 0 9.305950 9.80e-06
BAIAP2 135 -1.5745463 -1.5469382 0 9.076493 1.67e-05
PCDHGB2 259 -0.7588482 -0.6212502 0 9.033889 1.84e-05
GRIN2D 39 -2.3740747 -2.1138105 0 8.952001 2.22e-05
PCDHGA4 273 -0.7293561 -0.5978260 0 8.885595 2.59e-05 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
395 Expression and translocation of olfactory receptors 311 0.0000000 0.6055154 0.0000000
840 Olfactory Signaling Pathway 318 0.0000000 0.5916236 0.0000000
1416 Transcriptional regulation of testis differentiation 12 0.0003966 -0.5904425 0.0215028
276 Defective B3GAT3 causes JDSSDHD 17 0.0002011 -0.5206830 0.0132711
1493 mRNA Editing 10 0.0044231 0.5197132 0.0883446
277 Defective B4GALT7 causes EDS, progeroid type 17 0.0003578 -0.4999203 0.0208926
509 Glucuronidation 19 0.0003426 0.4744077 0.0208038
1490 eNOS activation 11 0.0068817 -0.4705115 0.1145247
274 Defective B3GALT6 causes EDSP2 and SEMDJL1 17 0.0008731 -0.4661973 0.0326638
445 Formation of apoptosome 10 0.0107853 -0.4655434 0.1249973
1115 Regulation of the apoptosome activity 10 0.0107853 -0.4655434 0.1249973
136 CD28 dependent Vav1 pathway 11 0.0078181 0.4630801 0.1145247
1484 Zinc influx into cells by the SLC39 gene family 10 0.0135247 -0.4509503 0.1387193
96 Assembly Of The HIV Virion 14 0.0035803 -0.4495661 0.0787669
909 Phosphorylation of CD3 and TCR zeta chains 20 0.0006963 0.4379158 0.0310875
700 Membrane binding and targetting of GAG proteins 12 0.0091054 -0.4347510 0.1201796
1311 Synthesis And Processing Of GAG, GAGPOL Polyproteins 12 0.0091054 -0.4347510 0.1201796
900 Phase 4 - resting membrane potential 19 0.0011119 -0.4320004 0.0364228
35 Activation of AMPK downstream of NMDARs 10 0.0184573 -0.4302593 0.1621296
1429 Translocation of ZAP-70 to Immunological synapse 17 0.0023161 0.4266904 0.0606186 
#mitch_report(mres,outfile="gmeawg_mitch_nat_vs_fz.html",overwrite=FALSE)
# Promoter
dm <- nat_vs_fz$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
234473 CD72 -17.81013
107155 SLC25A33 -17.30676
286730 TSPYL5;TSPYL5 -16.86416
358320 FGF9 -16.82315
34194 KCTD21;USP35 -16.54969
312054 ASH1L;LOC645676 -16.42457
398413 IRAK3;IRAK3;IRAK3;IRAK3 -16.29557
138436 XPO7;XPO7 -16.14727
364043 CD320;CD320 -16.08581
196471 UHRF1;UHRF1 -15.61601
235315 E2F1 -15.48926
268273 GMPPB;GMPPB;GMPPB;GMPPB -15.33406
11885 RAD54L;RAD54L;RAD54L -15.32834
304786 RPL23AP82;RABL2B;RABL2B;RABL2B;RPL23AP82;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B;RABL2B -15.29932
93032 MYO9A;SENP8;SENP8 -15.15397
239889 QARS -15.11431
342396 DIDO1;DIDO1;C20orf11;DIDO1 -15.06928
55372 HTR7P;HEBP1 -14.99003
283544 WDR1;WDR1;WDR1;WDR1 -14.94089
169177 DONSON;DONSON -14.85326
261873 HIST1H1C -14.75838
96919 -14.71827
338499 CCDC28B -14.54160
55136 -14.53173
356507 LOC100134713;NDUFB2 -14.48469
372380 RBCK1;RBCK1 -14.48077
32034 PRR7;PRR7 -14.45276
272880 GFOD1;C6orf114 -14.44872
192069 PPIF;PPIF -14.39409
315613 DDHD2;DDHD2;DDHD2;DDHD2;DDHD2 -14.38782
389530 GYS1;GYS1;RUVBL2;GYS1 -14.36816
319883 PSTPIP2;PSTPIP2 -14.36424
395530 BRPF1;BRPF1 -14.35557
381817 AKIRIN1;AKIRIN1 -14.30774
260863 ORC3L;ORC3L;RARS2 -14.29216
207462 MGMT -14.28081
228488 RALGAPB -14.27322
176371 ZNF554 -14.24819
178734 WBP2 -14.20084
154230 CCNDBP1;CCNDBP1;CCNDBP1;CCNDBP1;CCNDBP1 -14.19670
264459 SEPHS2 -14.12409
114200 CREM;CREM;CREM;CREM;CREM;CREM -14.07973
221706 MEA1;KLHDC3 -14.02645
312136 PNPLA8 -14.02219
255870 RBAK -14.01449
374812 AGPAT3 -13.98871
388254 FARSB -13.98249
127739 MED16 -13.90935
117648 SCARB2;SCARB2 -13.84914
336088 RNF216L;RNF216L;RNF216L -13.84156 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 36.885 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res ,file="estill_gmeapr_nat_vs_fz.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
PEG10 61 -3.579106 -3.777225 0.00e+00 10.835609 0.0000002
SGCE 58 -3.504764 -3.699541 0.00e+00 10.330397 0.0000005
FAM50B 29 -4.366856 -4.647860 0.00e+00 8.127810 0.0000768
RASA3 34 -2.479769 -2.181862 2.00e-07 6.693690 0.0020872
MGC23284 27 -3.501529 -3.170076 6.00e-07 6.193311 0.0066055
PCNA 22 -3.289215 -2.827303 1.00e-06 6.020600 0.0098305
FAM134C 22 -3.788481 -3.287859 1.00e-06 6.020600 0.0098305
TUBG1 22 -3.788481 -3.287859 1.00e-06 6.020600 0.0098305
L3MBTL 22 -3.093086 -2.927800 1.00e-06 6.020600 0.0098305
SKIV2L2 20 -3.187368 -2.775607 3.80e-06 5.418540 0.0393066
DHX29 20 -3.187368 -2.775607 3.80e-06 5.418540 0.0393066
CYP51A1 20 -2.489290 -2.571870 3.80e-06 5.418540 0.0393066
NFKB2 24 -2.811794 -2.971591 3.90e-06 5.405176 0.0405232
ST7OT4 22 -2.703682 -2.387789 4.80e-06 5.321630 0.0491142
ST7OT1 22 -2.703682 -2.387789 4.80e-06 5.321630 0.0491142
ST7 22 -2.703682 -2.387789 4.80e-06 5.321630 0.0491142
VARS2 40 -1.646557 -1.165145 4.90e-06 5.306906 0.0507931
MGMT 19 -2.855332 -2.076846 7.60e-06 5.117510 0.0785522
C14orf21 19 -2.513512 -2.520331 7.60e-06 5.117510 0.0785522
DHRS1 19 -2.513512 -2.520331 7.60e-06 5.117510 0.0785522
RPP21 35 -2.019140 -2.164256 1.19e-05 4.925077 0.1223109
HTATIP2 17 -2.250460 -2.075549 1.53e-05 4.816480 0.1570435
HCG4P6 17 -2.277746 -2.253528 1.53e-05 4.816480 0.1570435
MKKS 17 -1.809999 -1.755004 1.53e-05 4.816480 0.1570435
LTA 17 -2.185776 -2.044932 1.53e-05 4.816480 0.1570435
CEPT1 17 -2.238415 -2.171278 1.53e-05 4.816480 0.1570435
DRAM2 17 -2.238415 -2.171278 1.53e-05 4.816480 0.1570435
ZBTB12 34 -2.536799 -2.378804 1.55e-05 4.809258 0.1595839
MAP3K6 18 -2.393914 -2.042237 2.29e-05 4.640389 0.2354050
LOC100129716 18 -3.264461 -3.428635 2.29e-05 4.640389 0.2354050
ARRDC3 18 -3.264461 -3.428635 2.29e-05 4.640389 0.2354050
DNAJC30 19 -3.198544 -3.192469 2.67e-05 4.573442 0.2745590
WBSCR22 19 -3.198544 -3.192469 2.67e-05 4.573442 0.2745590
MMAB 19 -2.579095 -2.529525 2.67e-05 4.573442 0.2745590
MVK 19 -2.579095 -2.529525 2.67e-05 4.573442 0.2745590
CCDC96 16 -4.215941 -4.311240 3.05e-05 4.515450 0.3136597
TADA2B 16 -4.215941 -4.311240 3.05e-05 4.515450 0.3136597
SNX27 17 -2.730830 -2.380222 3.05e-05 4.515450 0.3136597
MRPL46 17 -3.343246 -3.640666 3.05e-05 4.515450 0.3136597
MRPS11 17 -3.343246 -3.640666 3.05e-05 4.515450 0.3136597
PRKCZ 16 -2.830503 -2.940501 3.05e-05 4.515450 0.3136597
NDUFA13 16 -1.805998 -1.653757 3.05e-05 4.515450 0.3136597
TSSK6 16 -1.805998 -1.653757 3.05e-05 4.515450 0.3136597
ELMO1 17 -2.242287 -2.028519 3.05e-05 4.515450 0.3136597
AFAP1 17 -1.932913 -1.920443 3.05e-05 4.515450 0.3136597
HOXA4 16 -2.672709 -2.675896 3.05e-05 4.515450 0.3136597
PRDM1 16 -1.694935 -1.899724 3.05e-05 4.515450 0.3136597
LRRC61 20 -2.760903 -2.555054 3.62e-05 4.440816 0.3720360
ACTR3C 20 -2.760903 -2.555054 3.62e-05 4.440816 0.3720360
PRRT1 20 -1.811931 -2.039721 3.62e-05 4.440816 0.3720360 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1077 Termination of O-glycan biosynthesis 10 0.0000617 0.7314374 0.0735852
553 Methylation 10 0.0091969 -0.4756673 0.3844710
677 PRC2 methylates histones and DNA 11 0.0084279 -0.4587371 0.3844710
313 FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes 14 0.0031004 -0.4565561 0.2639753
1166 Zinc transporters 11 0.0141929 -0.4270398 0.3844710
1138 Triglyceride catabolism 11 0.0258740 -0.3880006 0.3844710
736 Purine ribonucleoside monophosphate biosynthesis 10 0.0390972 -0.3768029 0.3952599
30 Activation of G protein gated Potassium channels 11 0.0307236 0.3762553 0.3844710
341 G protein gated Potassium channels 11 0.0307236 0.3762553 0.3844710
443 Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 11 0.0307236 0.3762553 0.3844710
340 G beta:gamma signalling through PLC beta 12 0.0257542 0.3718005 0.3844710
719 Presynaptic function of Kainate receptors 12 0.0257542 0.3718005 0.3844710
1159 Vitamin B5 (pantothenate) metabolism 11 0.0330779 0.3711195 0.3844710
214 Defective pyroptosis 10 0.0555846 -0.3496166 0.4115090
972 Signaling by Hippo 11 0.0470527 -0.3458199 0.3952599
1085 Thromboxane signalling through TP receptor 13 0.0321831 0.3431740 0.3844710
1027 Suppression of phagosomal maturation 12 0.0408596 -0.3409701 0.3952599
931 Sensory processing of sound by outer hair cells of the cochlea 16 0.0186161 -0.3398441 0.3844710
1139 Triglyceride metabolism 16 0.0189022 -0.3390247 0.3844710
337 G beta:gamma signalling through BTK 10 0.0651816 0.3367854 0.4310181 
#mitch_report(mres,outfile="gmeapr_mitch_nat_vs_fz.html",overwrite=FALSE)
rm(nat_vs_fz)

nat_vs_iui

dm <- nat_vs_iui$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
321265 cg20757019 Unclassified chr2:95872891-95873548 Island -1.2757353 -3.916546 -18.26873 0 0 49.58088 T C
307250 cg19732469 PAPOLA Promoter_Associated chr14:96968154-96969371 Island -0.9731112 -4.543404 -17.79415 0 0 48.29726 T C
34194 cg01931797 KCTD21;USP35 Promoter_Associated chr11:77899564-77899990 Island -1.0722220 -4.325648 -16.89573 0 0 45.78990 T C
179618 cg10992925 SEMA3F Unclassified chr3:50191971-50193130 Island -0.8632152 -3.170265 -16.42057 0 0 44.42176 T C
196471 cg12159575 UHRF1;UHRF1 Promoter_Associated chr19:4909262-4910256 S_Shore -1.2304453 -4.432795 -16.00132 0 0 43.18988 T C
66567 cg03817939 FAM176A;FAM176A chr2:75787717-75788312 Island -1.1610466 -4.117368 -15.96941 0 0 43.09515 T C
364043 cg23963136 CD320;CD320 Promoter_Associated chr19:8372597-8373302 Island -1.2706488 -4.592594 -15.96813 0 0 43.09135 T C
268273 cg16905586 GMPPB;GMPPB;GMPPB;GMPPB Promoter_Associated chr3:49760863-49761895 Island -0.8468308 -3.483195 -15.85851 0 0 42.76490 T C
281209 cg17854641 SYT3;SYT3;SYT3 chr19:51128325-51128793 N_Shore -0.7242533 1.985801 -15.64944 0 0 42.13778 T C
102951 cg06055730 chr6:136571120-136571814 S_Shelf -0.7330056 1.315972 -15.36636 0 0 41.27921 T C
298796 cg19110428 chr20:30326913-30327430 N_Shelf -1.4349962 1.769924 -15.21599 0 0 40.81869 T C
221706 cg13871588 MEA1;KLHDC3 Promoter_Associated chr6:42981408-42982077 Island -1.0473408 -4.633890 -15.19745 0 0 40.76169 T C
176371 cg10769393 ZNF554 Promoter_Associated chr19:2819630-2820295 Island -1.3531381 -3.674154 -14.97262 0 0 40.06678 T C
26062 cg01447112 Unclassified_Cell_type_specific chr7:6703503-6704075 Island -1.1123640 -3.588866 -14.92887 0 0 39.93073 T C
1110 cg00053536 CROCC chr1:17292904-17293115 N_Shore -0.8334969 2.231460 -14.91951 0 0 39.90159 T C
222143 cg13896861 SPTLC1;SPTLC1 chr9:94877272-94877782 S_Shore -0.5666608 1.155556 -14.91036 0 0 39.87309 T C
174319 cg10620911 AGPAT1;AGPAT1 OpenSea -0.8097543 1.458894 -14.90018 0 0 39.84139 T C
138526 cg08265790 SPRY4;SPRY4 Promoter_Associated chr5:141703749-141705023 Island -1.0913534 -3.659776 -14.86346 0 0 39.72685 T C
138436 cg08260549 XPO7;XPO7 Promoter_Associated chr8:21776842-21777942 Island -1.0171484 -3.999537 -14.83076 0 0 39.62470 T C
279529 cg17739026 PIGV Promoter_Associated chr1:27114118-27114692 Island -0.8795174 -3.704498 -14.81190 0 0 39.56574 T C
50066 cg02853781 ALDH4A1;ALDH4A1;ALDH4A1;ALDH4A1 Promoter_Associated chr1:19228828-19229634 Island -1.1547823 -4.774982 -14.73375 0 0 39.32082 T C
107155 cg06347499 SLC25A33 Promoter_Associated chr1:9599350-9600444 Island -1.1418350 -4.164527 -14.72408 0 0 39.29044 T C
103289 cg06079273 UQCRB Promoter_Associated OpenSea -0.9036707 -4.463942 -14.70187 0 0 39.22064 T C
312054 cg20064047 ASH1L;LOC645676 Promoter_Associated chr1:155531914-155533280 Island -1.0700658 -4.489803 -14.68497 0 0 39.16750 T C
344717 cg22583711 PAXIP1;LOC202781 Promoter_Associated chr7:154794017-154795750 Island -0.7162428 -3.825192 -14.58505 0 0 38.85245 T C
342136 cg22375623 IDH3A chr15:78441495-78442261 S_Shelf -0.7784733 1.723245 -14.45604 0 0 38.44359 T C
50084 cg02854490 OpenSea -0.8926530 2.349651 -14.45397 0 0 38.43701 T C
55372 cg03157633 HTR7P;HEBP1 Promoter_Associated chr12:13154088-13154866 Island -1.0530113 -4.315815 -14.42068 0 0 38.33112 T C
13871 cg00756450 GALK2;GALK2 OpenSea -1.4529012 2.101861 -14.42062 0 0 38.33094 T C
291292 cg18555811 HES1 Unclassified chr3:193854575-193856015 N_Shore -1.1459694 -4.281648 -14.40992 0 0 38.29689 T C
195450 cg12089543 C22orf40 Unclassified chr22:46645764-46646957 Island -0.9180891 -4.412665 -14.40280 0 0 38.27421 T C
392514 cg26020008 chr20:48531603-48532316 S_Shelf -0.6683636 1.366599 -14.35542 0 0 38.12311 T C
110655 cg06571075 MACROD2 chr20:13975768-13976287 Island -1.1744233 -4.487541 -14.26620 0 0 37.83775 T C
374817 cg24714100 HCG18;HCG18 chr6:30294169-30295071 N_Shelf -1.0393367 1.340146 -14.22801 0 0 37.71526 T C
202957 cg12636108 GPRIN1 Unclassified chr5:176036458-176037557 Island -0.9399768 -4.142972 -14.20192 0 0 37.63148 T C
266554 cg16774013 NFATC1;NFATC1;NFATC1;NFATC1;NFATC1 chr18:77153292-77160759 Island -1.1666900 -2.673373 -14.19186 0 0 37.59916 T C
313863 cg20206224 POLH;XPO5;XPO5 Promoter_Associated chr6:43543124-43544076 Island -0.8295587 -4.065363 -14.13464 0 0 37.41496 T C
344487 cg22562194 TTYH2;MGC16275 Promoter_Associated chr17:72209669-72210290 N_Shore -1.1107615 -4.090680 -14.09777 0 0 37.29603 T C
169177 cg10277546 DONSON;DONSON Promoter_Associated chr21:34960388-34961252 Island -0.9625450 -4.407189 -14.05292 0 0 37.15111 T C
418216 ch.3.3303606F PRKCI OpenSea -1.0829538 -1.345894 -14.01107 0 0 37.01561 T C
265729 cg16717099 FLOT1 Promoter_Associated chr6:30710307-30712440 Island -1.0741313 -4.268754 -13.99690 0 0 36.96969 T C
267712 cg16863872 PWP2 Promoter_Associated chr21:45526956-45527813 Island -0.9495893 -4.371513 -13.98528 0 0 36.93199 T C
80305 cg04645421 Unclassified chr5:108063600-108064072 Island -0.6275850 -3.946463 -13.94178 0 0 36.79076 T C
255870 cg16080015 RBAK Promoter_Associated chr7:5085411-5086342 Island -0.9596506 -4.200222 -13.94106 0 0 36.78843 T C
342396 cg22394521 DIDO1;DIDO1;C20orf11;DIDO1 Promoter_Associated chr20:61568678-61569916 Island -0.9813518 -4.237686 -13.88558 0 0 36.60789 T C
157563 cg09510269 HCG18;HCG18 chr6:30294169-30295071 N_Shore -0.7753083 1.849845 -13.84967 0 0 36.49080 T C
202084 cg12581662 ZNF565;ZNF146;ZNF146;ZNF565;ZNF146;ZNF146;ZNF146 Unclassified chr19:36705433-36706262 Island -0.9166685 -4.265901 -13.81200 0 0 36.36780 T C
11885 cg00645897 RAD54L;RAD54L;RAD54L Promoter_Associated OpenSea -1.1086879 -4.901097 -13.79309 0 0 36.30598 T C
234473 cg14572967 CD72 Promoter_Associated chr9:35616980-35617324 Island -1.1000234 -4.480695 -13.77429 0 0 36.24444 T C
376676 cg24846791 TRIM31 chr6:30071225-30071428 S_Shelf -0.9930862 1.520722 -13.68481 0 0 35.95097 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 54.222 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_nat_vs_iui.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
TNXB 543 -1.5949694 -1.8765126 0 45.602520 0.0e+00
PRDM16 608 -1.0925212 -1.1697485 0 25.186696 0.0e+00
COL11A2 226 -2.0392510 -2.2217727 0 23.155435 0.0e+00
PCDHGA2 319 -0.8652608 -0.7630974 0 18.443301 0.0e+00
PCDHGA3 305 -0.8931604 -0.8134303 0 18.309441 0.0e+00
PCDHGA1 327 -0.8397635 -0.7586245 0 17.930740 0.0e+00
PCDHGB1 287 -0.8972595 -0.8134303 0 17.061663 0.0e+00
PCDHGA4 273 -0.9067390 -0.8164445 0 16.737998 0.0e+00
PCDHGB2 259 -0.9339640 -0.8396905 0 16.663914 0.0e+00
PCDHGA5 247 -0.9638267 -0.8404172 0 16.580665 0.0e+00
PCDHGB3 230 -0.9799763 -0.8559937 0 16.212025 0.0e+00
BLCAP 119 -2.0250971 -1.9704521 0 15.345126 0.0e+00
PCDHGA6 220 -0.9606848 -0.8403847 0 14.927304 0.0e+00
GALNT9 234 -1.4177646 -1.6187758 0 14.833685 0.0e+00
MEGF6 133 -1.9112771 -2.1437150 0 13.915015 0.0e+00
HCCA2 245 -1.2182562 -1.3078976 0 13.770913 0.0e+00
INS-IGF2 138 -1.7286581 -1.7701813 0 13.678883 0.0e+00
PCDHGA7 205 -0.9366760 -0.8396905 0 13.312057 0.0e+00
KCNQ1 302 -1.0431908 -1.1908437 0 12.833543 0.0e+00
TP73 123 -1.8726684 -2.0319252 0 12.723270 0.0e+00
CACNA1H 159 -1.5016215 -1.3559426 0 12.033255 0.0e+00
SEPT9 160 -1.4089641 -1.5906425 0 11.909158 0.0e+00
GNAS 190 -1.2702504 -1.2288307 0 11.858412 0.0e+00
PLEC1 145 -1.7697250 -1.8905745 0 11.847196 0.0e+00
PCDHGB4 193 -0.9128670 -0.8098358 0 11.779683 0.0e+00
SLC44A4 96 -1.9648722 -2.1324385 0 11.568661 1.0e-07
GPR123 94 -1.9466597 -2.0805711 0 11.332620 1.0e-07
RNF39 86 -1.5329180 -1.2413464 0 11.147281 1.0e-07
MAD1L1 687 -0.6614104 -0.6234768 0 10.922448 2.0e-07
BAHCC1 109 -1.5844648 -1.5888006 0 10.860104 3.0e-07
OBSCN 127 -1.7805221 -1.8448699 0 10.709737 4.0e-07
PAX6 103 -1.9941644 -1.9523264 0 10.524972 6.0e-07
H19 61 -3.2994755 -3.5646852 0 10.494332 6.0e-07
SORCS2 186 -1.0573882 -1.2665494 0 10.351955 9.0e-07
ZBTB12 76 -2.1825647 -2.0495403 0 10.306029 1.0e-06
ZIC1 46 -1.9670342 -2.0007006 0 10.170686 1.3e-06
ASCL2 49 -2.0831970 -2.1603956 0 10.167022 1.4e-06
TFAP2B 39 -2.3082396 -2.1237264 0 10.160386 1.4e-06
ATM 49 -2.1597135 -1.9705226 0 10.057429 1.7e-06
BAI1 82 -2.1351525 -2.5702625 0 9.988255 2.0e-06
VENTX 45 -2.0890059 -1.5503587 0 9.936755 2.3e-06
NNAT 49 -1.9542592 -1.9704521 0 9.792661 3.2e-06
GNASAS 88 -1.7659346 -1.9375958 0 9.683044 4.1e-06
IDUA 44 -2.5074777 -2.7233165 0 9.635725 4.6e-06
IGF2 111 -1.5201069 -1.5993488 0 9.586554 5.2e-06
SOX2OT 86 -1.6211621 -1.7894346 0 9.513325 6.1e-06
LOC645323 83 -1.7929436 -1.9381620 0 9.512006 6.1e-06
HOXC4 120 -1.4277263 -1.2545752 0 9.488780 6.5e-06
CHD5 75 -1.9525754 -2.0584175 0 9.370779 8.5e-06
CAMTA1 237 -1.1094068 -1.1687757 0 9.337729 9.1e-06 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
395 Expression and translocation of olfactory receptors 311 0.0000000 0.6791321 0.0000000
840 Olfactory Signaling Pathway 318 0.0000000 0.6625631 0.0000000
1416 Transcriptional regulation of testis differentiation 12 0.0004519 -0.5846916 0.0053587
1490 eNOS activation 11 0.0010186 -0.5719613 0.0094859
136 CD28 dependent Vav1 pathway 11 0.0010398 0.5709492 0.0095086
562 Hormone ligand-binding receptors 12 0.0008630 0.5553605 0.0086272
897 Pexophagy 11 0.0016058 -0.5492477 0.0132482
909 Phosphorylation of CD3 and TCR zeta chains 20 0.0000307 0.5382771 0.0006045
1508 p75NTR recruits signalling complexes 12 0.0013907 -0.5328335 0.0118596
509 Glucuronidation 19 0.0000912 0.5183941 0.0014424
115 Beta defensins 28 0.0000027 0.5120553 0.0000981
364 ER Quality Control Compartment (ERQC) 20 0.0000820 -0.5085947 0.0013383
96 Assembly Of The HIV Virion 14 0.0010929 -0.5039589 0.0098166
1484 Zinc influx into cells by the SLC39 gene family 10 0.0064050 -0.4978085 0.0314652
371 ERKs are inactivated 13 0.0020266 -0.4942861 0.0154591
296 Defensins 36 0.0000004 0.4894566 0.0000156
700 Membrane binding and targetting of GAG proteins 12 0.0034304 -0.4877878 0.0217880
1311 Synthesis And Processing Of GAG, GAGPOL Polyproteins 12 0.0034304 -0.4877878 0.0217880
130 Butyrophilin (BTN) family interactions 12 0.0034839 0.4869853 0.0219440
161 Calnexin/calreticulin cycle 25 0.0000267 -0.4851069 0.0005485 
#mitch_report(mres,outfile="gmeawg_mitch_nat_vs_GIFT.html",overwrite=FALSE)
# Promoter
dm <- nat_vs_iui$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
307250 PAPOLA -17.79415
34194 KCTD21;USP35 -16.89573
196471 UHRF1;UHRF1 -16.00132
364043 CD320;CD320 -15.96813
268273 GMPPB;GMPPB;GMPPB;GMPPB -15.85851
221706 MEA1;KLHDC3 -15.19745
176371 ZNF554 -14.97262
138526 SPRY4;SPRY4 -14.86346
138436 XPO7;XPO7 -14.83076
279529 PIGV -14.81190
50066 ALDH4A1;ALDH4A1;ALDH4A1;ALDH4A1 -14.73375
107155 SLC25A33 -14.72408
103289 UQCRB -14.70187
312054 ASH1L;LOC645676 -14.68497
344717 PAXIP1;LOC202781 -14.58505
55372 HTR7P;HEBP1 -14.42068
313863 POLH;XPO5;XPO5 -14.13464
344487 TTYH2;MGC16275 -14.09777
169177 DONSON;DONSON -14.05292
265729 FLOT1 -13.99690
267712 PWP2 -13.98528
255870 RBAK -13.94106
342396 DIDO1;DIDO1;C20orf11;DIDO1 -13.88558
11885 RAD54L;RAD54L;RAD54L -13.79309
234473 CD72 -13.77429
228488 RALGAPB -13.60279
293446 HIRA;MRPL40;MRPL40 -13.57980
127739 MED16 -13.57462
5060 POLR1C;YIPF3;POLR1C;POLR1C;POLR1C -13.49643
81402 ZZZ3 -13.33780
372380 RBCK1;RBCK1 -13.27147
292848 RELL2;RELL2;HDAC3 -13.19071
283544 WDR1;WDR1;WDR1;WDR1 -13.16660
354943 C19orf54;SNRPA -13.11191
175816 KDELR2;KDELR2 -13.05999
260863 ORC3L;ORC3L;RARS2 -13.01873
336088 RNF216L;RNF216L;RNF216L -12.98035
202495 H1FX;C3orf47 -12.92260
363442 CATSPERG -12.91615
22257 SNX2 -12.90373
113813 CAMTA1;CAMTA1 -12.86759
154230 CCNDBP1;CCNDBP1;CCNDBP1;CCNDBP1;CCNDBP1 -12.82641
116386 KIAA1841;KIAA1841 -12.74846
235315 E2F1 -12.74362
304268 C14orf43 -12.66522
16965 MGC23284;SNAI3 -12.64107
286730 TSPYL5;TSPYL5 -12.61594
315613 DDHD2;DDHD2;DDHD2;DDHD2;DDHD2 -12.60825
192023 CAMSAP1L1 -12.56167
338499 CCDC28B -12.55043 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 33.077 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res ,file="estill_gmeapr_nat_vs_iui.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
RPP21 35 -2.374046 -2.358891 0.0e+00 9.757899 0.0000018
KILLIN 54 -2.371495 -2.183014 0.0e+00 8.800757 0.0000163
PTEN 53 -2.396813 -2.205314 0.0e+00 8.639743 0.0000236
BAT5 36 -2.198376 -2.220584 0.0e+00 8.494657 0.0000330
C6orf48 42 -2.171606 -2.236395 0.0e+00 8.462331 0.0000356
RNF5P1 28 -3.295595 -3.072394 0.0e+00 8.127810 0.0000768
RNF5 28 -3.295595 -3.072394 0.0e+00 8.127810 0.0000768
ZBTB12 34 -2.432674 -2.039177 0.0e+00 7.797269 0.0001644
RASA3 34 -2.454874 -2.534050 0.0e+00 7.797269 0.0001644
MGC23284 27 -3.385014 -2.722472 0.0e+00 7.525750 0.0003071
ANKHD1-EIF4EBP3 26 -3.001112 -2.494776 0.0e+00 7.525750 0.0003071
ZBTB9 35 -2.340836 -2.017341 0.0e+00 7.428840 0.0003838
GNL1 55 -2.232146 -2.362043 0.0e+00 7.380510 0.0004289
AGPAT1 34 -3.094480 -3.050485 0.0e+00 7.364616 0.0004449
TRIM27 53 -1.792429 -1.784421 0.0e+00 7.327545 0.0004845
DDAH2 39 -2.443252 -2.650839 1.0e-07 7.269142 0.0005541
FLOT1 68 -2.099289 -2.044199 1.0e-07 7.246761 0.0005834
FAM50B 29 -2.642246 -2.608388 1.0e-07 7.150086 0.0007288
BRD2 58 -1.949749 -2.419026 1.0e-07 7.111506 0.0007964
ATM 32 -2.016940 -2.017899 1.0e-07 7.015960 0.0009923
NPAT 32 -2.016940 -2.017899 1.0e-07 7.015960 0.0009923
VARS2 40 -1.767922 -1.674643 1.0e-07 6.984348 0.0010670
BLCAP 47 -2.358040 -2.295024 1.0e-07 6.935307 0.0011944
PAN2 23 -2.951208 -2.405971 2.0e-07 6.622660 0.0024533
SNORD48 23 -2.709548 -2.685054 2.0e-07 6.622660 0.0024533
MICA 40 -2.267701 -2.365748 3.0e-07 6.503051 0.0032306
RAB1B 58 -2.342748 -2.617105 3.0e-07 6.456270 0.0035976
DAXX 38 -2.281963 -2.567897 4.0e-07 6.384626 0.0042425
MTIF3 22 -3.268386 -2.865420 5.0e-07 6.321630 0.0049043
CFLAR 23 -2.048293 -1.967003 5.0e-07 6.321630 0.0049043
PRR3 40 -2.361156 -2.550548 6.0e-07 6.233466 0.0060069
L3MBTL 22 -2.711772 -2.328640 1.0e-06 6.020600 0.0098057
TUBB 27 -1.904607 -1.862300 1.0e-06 5.981682 0.0107239
HLA-E 35 -1.809158 -1.730772 1.1e-06 5.956289 0.0113685
PHF1 28 -2.744082 -2.419923 1.3e-06 5.899923 0.0129428
CENPT 29 -2.956126 -2.902679 1.4e-06 5.859466 0.0142050
FAM134C 22 -3.293016 -3.112716 1.4e-06 5.844509 0.0147014
TUBG1 22 -3.293016 -3.112716 1.4e-06 5.844509 0.0147014
RUFY1 22 -1.698783 -1.035319 1.4e-06 5.844509 0.0147014
MKLN1 25 -2.475844 -2.070396 1.5e-06 5.826780 0.0153095
RING1 28 -2.651814 -2.123128 1.5e-06 5.811839 0.0158437
BAT3 53 -1.893880 -2.026428 1.7e-06 5.757295 0.0179622
TBCCD1 20 -2.458405 -2.329369 1.9e-06 5.719570 0.0195904
SKIV2L2 20 -2.977593 -2.775134 1.9e-06 5.719570 0.0195904
DHX29 20 -2.977593 -2.775134 1.9e-06 5.719570 0.0195904
ACTR3C 20 -2.521504 -2.131852 1.9e-06 5.719570 0.0195904
LRRC61 20 -2.521504 -2.131852 1.9e-06 5.719570 0.0195904
MATR3 25 -2.303645 -2.423867 2.0e-06 5.706206 0.0201927
ANKRD11 27 -1.987213 -2.040937 2.0e-06 5.690059 0.0209556
PCNA 22 -2.830167 -2.241411 2.4e-06 5.622660 0.0244713 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1077 Termination of O-glycan biosynthesis 10 0.0046802 0.5165389 0.1224399
1034 Synthesis of Leukotrienes (LT) and Eoxins (EX) 10 0.0128531 0.4543822 0.1701514
1056 TNFR1-induced proapoptotic signaling 12 0.0100829 -0.4290279 0.1576478
274 ER Quality Control Compartment (ERQC) 18 0.0023417 -0.4143975 0.0996891
142 Cholesterol biosynthesis 20 0.0014754 -0.4107840 0.0660382
553 Methylation 10 0.0245708 -0.4106086 0.2177112
279 ERKs are inactivated 11 0.0220176 -0.3988281 0.2050390
447 InlB-mediated entry of Listeria monocytogenes into host cell 11 0.0246151 -0.3913980 0.2177112
112 Calnexin/calreticulin cycle 23 0.0014958 -0.3826340 0.0660382
376 Glucagon-type ligand receptors 13 0.0172303 0.3815907 0.1801623
116 Cargo concentration in the ER 19 0.0041043 -0.3804362 0.1193245
150 Class A/1 (Rhodopsin-like receptors) 45 0.0000120 0.3774423 0.0047644
139 Chaperone Mediated Autophagy 12 0.0239053 -0.3766301 0.2175198
587 N-glycan trimming in the ER and Calnexin/Calreticulin cycle 32 0.0002552 -0.3737112 0.0283483
371 Generation of second messenger molecules 16 0.0096698 0.3737071 0.1576478
607 Negative regulation of FGFR1 signaling 17 0.0085485 -0.3684755 0.1520876
608 Negative regulation of FGFR2 signaling 17 0.0085485 -0.3684755 0.1520876
609 Negative regulation of FGFR3 signaling 17 0.0085485 -0.3684755 0.1520876
610 Negative regulation of FGFR4 signaling 17 0.0085485 -0.3684755 0.1520876
1022 Spry regulation of FGF signaling 15 0.0135658 -0.3682204 0.1701514 
#mitch_report(mres,outfile="gmeapr_mitch_nat_vs_GIFT.html",overwrite=FALSE)
rm(nat_vs_iui)

iui_vs_fx

dm <- iui_vs_fx$dma
head(dm,50) %>% kbl(caption = "Top significant genes with limma") %>% kable_paper("hover", full_width = F)
Top significant genes with limma
Row.names UCSC_RefGene_Name Regulatory_Feature_Group Islands_Name Relation_to_Island logFC AveExpr t P.Value adj.P.Val B unmeth meth
276287 cg17476421 ZNF14 Promoter_Associated chr19:19843482-19843943 S_Shore 0.4699052 -4.3368000 6.994529 0e+00 0.0001483 12.326273 T C
171967 cg10471644 TPI1;TPI1;TPI1 Promoter_Associated chr12:6976392-6977393 Island 0.4729359 -4.6532577 6.826697 0e+00 0.0001634 11.624493 T C
180034 cg11022944 PGGT1B Promoter_Associated_Cell_type_specific chr5:114598301-114598657 Island 0.6656076 -2.9879143 6.701950 0e+00 0.0001846 11.105965 T C
311754 cg20040772 MEPCE;ZCWPW1 Promoter_Associated chr7:100025804-100028002 Island 0.4475989 -4.2772196 6.652268 0e+00 0.0001846 10.900240 T C
321952 cg20811730 PRPF3 Promoter_Associated chr1:150293835-150294140 Island 0.5156218 -3.7183273 6.583572 0e+00 0.0002031 10.616557 T C
152708 cg09197288 IFI27L1;IFI27L1 chr14:94547001-94547665 S_Shelf -0.4183156 1.7649111 -6.501013 0e+00 0.0002480 10.276866 T C
162560 cg09852007 AMOTL2 Unclassified_Cell_type_specific chr3:134092257-134093741 Island 0.4979181 -3.8820413 6.427566 0e+00 0.0002553 9.975856 T C
367467 cg24185116 LYSMD2;TMOD2;TMOD2 Promoter_Associated_Cell_type_specific chr15:52043422-52044447 Island -0.4587449 -2.6788126 -6.390055 0e+00 0.0002553 9.822568 T C
289989 cg18462141 chr11:49872066-49872440 Island -0.6629113 1.5651083 -6.387896 0e+00 0.0002553 9.813753 T C
231038 cg14382070 chr9:68298596-68299115 Island -0.6446638 1.8241697 -6.364654 0e+00 0.0002553 9.718941 T C
283632 cg18029778 MLL5;MLL5;MLL5;MLL5;LOC100216545 Promoter_Associated chr7:104653119-104654966 Island 0.4132271 -3.9865935 6.332902 0e+00 0.0002553 9.589609 T C
95399 cg05577434 GGT1;GGT1;GGT1;GGT1 Promoter_Associated_Cell_type_specific OpenSea -0.3891894 -1.0538017 -6.330239 0e+00 0.0002553 9.578774 T C
10286 cg00556029 MARCKSL1 chr1:32800859-32802229 Island -0.5262236 -1.7385638 -6.325604 0e+00 0.0002553 9.559917 T C
383454 cg25341937 NUP153 Promoter_Associated chr6:17706292-17707339 Island 0.3920338 -4.2660919 6.310231 0e+00 0.0002553 9.497406 T C
227631 cg14191698 DHX16;DHX16 Promoter_Associated chr6:30640431-30640853 Island 0.5285340 -4.6231596 6.265968 0e+00 0.0002916 9.317729 T C
399670 cg26503018 SGCE;PEG10;SGCE;PEG10;SGCE Promoter_Associated chr7:94284858-94286527 Island -0.3037998 0.3365029 -6.243002 0e+00 0.0003035 9.224686 T C
402515 cg26687499 MSL2;MSL2 Promoter_Associated chr3:135914197-135916090 Island 0.3409157 -4.5927898 6.178166 0e+00 0.0003790 8.962687 T C
193868 cg11985632 SGCE;PEG10;SGCE;PEG10;SGCE Promoter_Associated chr7:94284858-94286527 Island -0.3450787 0.7429853 -6.164369 0e+00 0.0003790 8.907067 T C
143390 cg08579753 chr1:39174379-39174940 Island -0.3081793 0.3784427 -6.156124 0e+00 0.0003790 8.873850 T C
48186 cg02738677 OpenSea -0.6943381 2.0127771 -6.032186 0e+00 0.0006294 8.376626 T C
331567 cg21546286 chr11:48921725-48922742 S_Shore -0.4373427 0.5536174 -6.011301 0e+00 0.0006583 8.293229 T C
47584 cg02706910 ZNF254;ZNF254 Promoter_Associated OpenSea -0.1933204 -0.8851308 -5.986146 0e+00 0.0007033 8.192935 T C
321327 cg20762182 KIF23;KIF23 OpenSea -0.5668844 2.0248688 -5.971857 0e+00 0.0007172 8.136043 T C
75089 cg04324509 PCNP chr3:101292885-101293612 S_Shelf -0.4250664 2.3226282 -5.937100 0e+00 0.0008026 7.997884 T C
350679 cg23012288 FAM128A;LOC150776 Promoter_Associated chr2:132249335-132250975 Island 0.4522471 -5.4900200 5.892031 1e-07 0.0009418 7.819232 T C
51030 cg02905964 UQCRFS1 chr19:29703570-29704331 Island -0.2160784 -1.9022644 -5.845482 1e-07 0.0011133 7.635311 T C
241614 cg15050398 chr6:28831682-28832134 N_Shelf -0.4723720 0.5984604 -5.822005 1e-07 0.0011382 7.542788 T C
171660 cg10449522 PHF7;PHF7;PHF7;BAP1;PHF7 Promoter_Associated chr3:52443677-52445104 Island 0.3472632 -4.4156565 5.821824 1e-07 0.0011382 7.542076 T C
97953 cg05742286 chr12:94533729-94533952 Island -0.4978103 1.9056671 -5.812870 1e-07 0.0011382 7.506830 T C
82641 cg04791162 chr14:62331009-62331641 Island -0.4806811 2.1535327 -5.795971 1e-07 0.0011382 7.440372 T C
161006 cg09746604 chr3:15919450-15919653 Island -0.4470853 1.4721585 -5.793842 1e-07 0.0011382 7.432006 T C
168215 cg10212184 SORD OpenSea -0.3814796 1.9088864 -5.793533 1e-07 0.0011382 7.430792 T C
52905 cg03008165 OpenSea -0.6376154 2.1211817 -5.775339 1e-07 0.0011959 7.359350 T C
326548 cg21166544 OpenSea -0.6927664 0.0001843 -5.758533 1e-07 0.0012300 7.293445 T C
108105 cg06406294 GART;SON;GART;GART;GART;GART;GART;SON Unclassified chr21:34914303-34915906 Island 0.3047739 -3.9811818 5.755593 1e-07 0.0012300 7.281927 T C
192293 cg11873147 C1QL2 chr2:119914126-119916663 Island 0.3072489 -2.8948194 5.719224 1e-07 0.0013944 7.139627 T C
335435 cg21844316 Promoter_Associated chr22:36850893-36851466 Island 0.3612205 -4.7421912 5.714390 1e-07 0.0013944 7.120745 T C
358594 cg23567369 AP1G2 Promoter_Associated chr14:24036399-24037076 Island 0.3337873 -3.6989264 5.683659 1e-07 0.0014868 7.000863 T C
2717 cg00138804 OpenSea -0.3269675 0.5582524 -5.681993 1e-07 0.0014868 6.994373 T C
131231 cg07808983 ZNF737 Promoter_Associated OpenSea -0.2054923 -1.7186465 -5.681960 1e-07 0.0014868 6.994245 T C
27264 cg01520571 LHX1 chr17:35291899-35300875 Island 0.7653814 -2.4845133 5.664792 2e-07 0.0015636 6.927407 T C
237276 cg14751914 SMAD7 chr18:46474931-46479364 Island 0.5460008 -2.6704118 5.647784 2e-07 0.0016309 6.861285 T C
147779 cg08866780 APP;APP;APP;APP;APP Promoter_Associated chr21:27541893-27543524 Island 0.5665759 -3.5062151 5.641263 2e-07 0.0016309 6.835956 T C
83204 cg04828509 ARPC1A Unclassified chr7:98923235-98923975 Island 0.3482253 -4.4130842 5.638975 2e-07 0.0016309 6.827075 T C
94601 cg05521474 OpenSea -0.5809906 1.7229611 -5.625579 2e-07 0.0016905 6.775093 T C
154842 cg09332309 CAMTA2;CAMTA2;CAMTA2;CAMTA2 Promoter_Associated chr17:4890282-4890991 Island 0.3722923 -4.6264554 5.608088 2e-07 0.0017318 6.707310 T C
173822 cg10588211 chr1:162792176-162792574 Island -0.5254736 -2.4020304 -5.607040 2e-07 0.0017318 6.703254 T C
242251 cg15092368 chr1:143270158-143270509 Island -0.2979315 0.2682895 -5.605209 2e-07 0.0017318 6.696163 T C
402523 cg26687746 OpenSea -0.3555826 0.2576688 -5.594182 2e-07 0.0017798 6.653488 T C
102834 cg06046629 CACNA1D;CACNA1D;CACNA1D OpenSea -0.4586108 1.0964756 -5.579593 2e-07 0.0018582 6.597090 T C 
dm <- dm[,c("UCSC_RefGene_Name","t")]
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 61.526 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res,file="estill_gmeawg_iui_vs_fx.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
PRDM16 608 0.4385745 0.3973281 0e+00 21.153267 0.0000000
PCDHGA3 305 0.5940183 0.5897146 0e+00 18.182544 0.0000000
PCDHGA1 327 0.5508785 0.5804108 0e+00 17.304159 0.0000000
PCDHGB1 287 0.6089373 0.6219591 0e+00 17.169280 0.0000000
PCDHGA2 319 0.5548165 0.5804108 0e+00 16.864110 0.0000000
PCDHGA4 273 0.5930617 0.6074057 0e+00 15.658485 0.0000000
PCDHGB2 259 0.6122564 0.6148877 0e+00 15.443598 0.0000000
PCDHGA5 247 0.5809178 0.5897146 0e+00 13.837844 0.0000000
PCDHGB3 230 0.5658312 0.5985602 0e+00 12.262714 0.0000000
PCDHGA6 220 0.5550031 0.5985602 0e+00 11.302285 0.0000001
SGCE 88 -1.9064107 -2.0838868 0e+00 10.413896 0.0000008
PCDHGA7 205 0.5516167 0.5816837 0e+00 9.991462 0.0000020
PEG10 105 -1.5611915 -1.5303570 0e+00 9.323963 0.0000095
PCDHGB4 193 0.5497858 0.6074057 0e+00 9.225192 0.0000119
BRD2 167 0.6684407 0.7451061 0e+00 8.755132 0.0000350
GNL1 112 0.8020904 0.9452346 0e+00 8.749645 0.0000355
PCDHGA8 177 0.5597471 0.5897146 0e+00 8.576168 0.0000529
DIRAS3 31 -1.2818417 -1.2445989 0e+00 8.331930 0.0000928
COL11A2 226 0.4195144 0.5066791 0e+00 8.085483 0.0001637
AGPAT1 85 0.8031825 0.7830746 0e+00 8.012805 0.0001935
PFDN6 56 1.4242759 1.3929310 0e+00 7.957320 0.0002199
SLC3A2 43 1.1936264 0.9891532 0e+00 7.936218 0.0002308
GNAS 190 -0.5614363 -0.5727687 0e+00 7.916867 0.0002413
SDK1 278 -0.4188863 -0.4888606 0e+00 7.907220 0.0002467
PCDHGB5 161 0.5691042 0.6074057 0e+00 7.682284 0.0004142
WDR46 107 0.8206149 0.9584373 0e+00 7.674362 0.0004218
MEST 84 -0.8810070 -0.9469625 0e+00 7.644668 0.0004516
PSMB8 83 0.8882582 0.8713295 0e+00 7.601421 0.0004988
CSNK2B 81 1.0799405 1.2209388 0e+00 7.523400 0.0005970
MESTIT1 58 -1.1264091 -1.2411235 0e+00 7.432306 0.0007363
RPS18 62 1.2255584 1.2975516 0e+00 7.309103 0.0009777
BLCAP 119 0.6532798 0.6592217 1e-07 7.196533 0.0012669
PCDHGA9 148 0.5811799 0.6184234 1e-07 7.178960 0.0013192
CBX5 32 1.5166050 1.7273183 1e-07 7.104043 0.0015675
RNF5 46 1.1430781 1.3291248 1e-07 7.043384 0.0018024
HOXA5 51 -0.7204583 -0.7220168 1e-07 7.027430 0.0018697
MORG1 36 1.2639616 1.2053752 1e-07 6.901573 0.0024981
MRPS18B 55 1.4018536 1.5820501 1e-07 6.895133 0.0025353
GATA3 70 1.0217541 0.9440276 1e-07 6.871776 0.0026752
MEGF6 133 0.5081150 0.6246394 2e-07 6.814203 0.0030543
PCDHGB6 142 0.5866235 0.6023012 2e-07 6.798529 0.0031664
C6orf47 46 0.9423189 0.8510690 2e-07 6.783154 0.0032803
BAT3 90 0.8862833 0.8616504 2e-07 6.640987 0.0045505
RXRB 90 0.7812912 0.8702903 3e-07 6.594281 0.0050670
SNORD84 32 1.5950232 1.5111433 3e-07 6.525750 0.0059327
PPP1R10 75 1.0511974 1.2514823 4e-07 6.392777 0.0080576
HNRNPA1 26 1.7232258 1.8936173 4e-07 6.379622 0.0083050
MIMT1 23 -1.5577261 -1.6242622 5e-07 6.321630 0.0094910
FKBPL 46 1.0846770 0.9174721 6e-07 6.192524 0.0127760
GNASAS 88 -0.6810524 -0.7878476 8e-07 6.118760 0.0151404 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets, priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>% kbl(caption = "Top enriched gene sets with GMEA-Mitch") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch
set setSize pANOVA s.dist p.adjustANOVA
890 Peptide chain elongation 84 0.0000000 0.5862126 0.0000000
391 Eukaryotic Translation Elongation 88 0.0000000 0.5838196 0.0000000
1468 Viral mRNA Translation 84 0.0000000 0.5577783 0.0000000
393 Eukaryotic Translation Termination 87 0.0000000 0.5506062 0.0000000
1148 SARS-CoV-2 modulates host translation machinery 45 0.0000000 0.5470489 0.0000000
444 Formation of a pool of free 40S subunits 95 0.0000000 0.5434889 0.0000000
1129 Response of EIF2AK4 (GCN2) to amino acid deficiency 94 0.0000000 0.5342877 0.0000000
1187 Selenocysteine synthesis 87 0.0000000 0.5322758 0.0000000
321 Diseases associated with glycosylation precursor biosynthesis 15 0.0003997 0.5278291 0.0030641
816 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 89 0.0000000 0.5199919 0.0000000
959 Protein methylation 11 0.0028673 0.5190754 0.0173675
450 Formation of the ternary complex, and subsequently, the 43S complex 47 0.0000000 0.5087452 0.0000001
655 L13a-mediated translational silencing of Ceruloplasmin expression 104 0.0000000 0.4967104 0.0000000
488 GTP hydrolysis and joining of the 60S ribosomal subunit 105 0.0000000 0.4896724 0.0000000
1166 SRP-dependent cotranslational protein targeting to membrane 105 0.0000000 0.4873502 0.0000000
1457 Unwinding of DNA 11 0.0054904 0.4834184 0.0301970
162 Cap-dependent Translation Initiation 112 0.0000000 0.4753552 0.0000000
392 Eukaryotic Translation Initiation 112 0.0000000 0.4753552 0.0000000
964 Purine salvage 12 0.0047613 0.4705142 0.0266705
815 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 106 0.0000000 0.4636147 0.0000000 
#mitch_report(mres,outfile="gmeawg_mitch_nat_vs_GIFT.html",overwrite=FALSE)
# Promoter
dm <- iui_vs_fx$dma
dm <- dm[grep("Promoter_Associated",dm$Regulatory_Feature_Group),]
dm <- dm[,c("UCSC_RefGene_Name","t")]
head(dm,50) %>% kbl(caption = "Top significant promoters with limma") %>% kable_paper("hover", full_width = F)
Top significant promoters with limma
UCSC_RefGene_Name t
276287 ZNF14 6.994529
171967 TPI1;TPI1;TPI1 6.826697
180034 PGGT1B 6.701950
311754 MEPCE;ZCWPW1 6.652268
321952 PRPF3 6.583572
367467 LYSMD2;TMOD2;TMOD2 -6.390055
283632 MLL5;MLL5;MLL5;MLL5;LOC100216545 6.332902
95399 GGT1;GGT1;GGT1;GGT1 -6.330239
383454 NUP153 6.310231
227631 DHX16;DHX16 6.265968
399670 SGCE;PEG10;SGCE;PEG10;SGCE -6.243002
402515 MSL2;MSL2 6.178166
193868 SGCE;PEG10;SGCE;PEG10;SGCE -6.164369
47584 ZNF254;ZNF254 -5.986146
350679 FAM128A;LOC150776 5.892031
171660 PHF7;PHF7;PHF7;BAP1;PHF7 5.821824
335435 5.714390
358594 AP1G2 5.683659
131231 ZNF737 -5.681960
147779 APP;APP;APP;APP;APP 5.641263
154842 CAMTA2;CAMTA2;CAMTA2;CAMTA2 5.608088
140604 C5orf35 -5.573058
289843 C6orf70;TCTE3 5.565892
184895 LOC728723;ZBED3 5.560119
345529 FLJ45983;GATA3;GATA3;FLJ45983 5.542748
73754 FN3KRP 5.537093
343907 NOD1 5.504397
299130 KLF6;KLF6;KLF6;KLF6 5.485533
387859 ALDH16A1;ALDH16A1;PIH1D1;PIH1D1 5.479508
333398 5.433714
228289 AP3D1;AP3D1 5.404442
64002 TECPR1 5.359989
358525 FKBPL 5.359263
333146 SUDS3;SUDS3 5.323693
375011 ADC 5.299186
359939 MEA1;KLHDC3 5.232085
199645 ATP5L 5.228787
139964 RREB1;RREB1;RREB1;RREB1;RREB1;RREB1;RREB1 5.209525
88751 FDXACB1;C11orf1;FDXACB1 5.183670
239964 ADCK5 5.177728
146372 KIAA1826;KIAA1826 -5.169509
17758 C7orf57 5.158181
30541 ZNF395 -5.151573
31471 SPRED1 5.145833
138995 SGCE;PEG10;SGCE;PEG10;SGCE -5.132880
75287 ANKRD11 5.124669
274738 STK19;STK19;STK19;DOM3Z 5.105700
333130 5.100388
141072 UBB 5.092601
70186 PNKD;PNKD 5.079905 
hist(dm$t)

tic() ; gmea <- calc_sc(dm) ; time2 <- toc()
## 34.513 sec elapsed
df <- gmea[[1]]
res <- gmea[[2]]
write.table(res ,file="estill_gmeapr_iui_vs_fx.tsv")
head(res,50) %>% kbl(caption = "Top significant genes with GMEA") %>% kable_paper("hover", full_width = F)
Top significant genes with GMEA
nprobes mean median p-value(sc) sig fdr(sc)
AGPAT1 34 1.4661560 1.5618149 0.00e+00 9.933990 0.0000012
BLCAP 47 1.3746983 1.4067765 0.00e+00 8.987737 0.0000106
PSMB8 46 1.1991206 1.2307358 0.00e+00 8.838448 0.0000150
RNF5P1 28 1.5383797 1.6613885 0.00e+00 8.127810 0.0000768
RNF5 28 1.5383797 1.6613885 0.00e+00 8.127810 0.0000768
VPS52 32 1.5120246 1.6114491 1.00e-07 7.195209 0.0006576
RPS18 32 1.5120246 1.6114491 1.00e-07 7.195209 0.0006576
SGCE 58 -2.1308974 -2.2933017 1.00e-07 6.981536 0.0010754
PEG10 61 -2.0167628 -2.1679262 2.00e-07 6.751738 0.0018252
BAT3 53 1.2299006 1.1012516 3.00e-07 6.487437 0.0033540
GNL1 55 1.1400111 1.3727073 5.00e-07 6.274459 0.0054765
CUTA 55 1.0280726 0.9441747 2.20e-06 5.666020 0.0222280
BAT4 40 1.3216810 1.3806883 2.90e-06 5.534097 0.0301149
CSNK2B 40 1.3216810 1.3806883 2.90e-06 5.534097 0.0301149
TAPBP 72 0.8343815 0.8532833 3.20e-06 5.501104 0.0324856
RAB1B 58 0.8840351 0.9399132 4.20e-06 5.372004 0.0437270
MSH5 39 0.8483118 0.8685572 4.40e-06 5.356251 0.0453377
MAD2L1BP 23 1.2095951 1.0687379 4.50e-06 5.343906 0.0466404
MORG1 28 1.3466087 1.2259875 4.80e-06 5.321630 0.0490904
HNRNPUL1 24 1.2365363 1.2146205 5.10e-06 5.290221 0.0527670
IER3 42 1.0584429 0.8803432 6.50e-06 5.189613 0.0665165
GNB2L1 24 1.7498119 1.8091220 6.60e-06 5.183327 0.0674796
BAT2 34 1.4089461 1.4802960 7.20e-06 5.140130 0.0745295
MRPL2 18 1.8111094 1.9946374 7.60e-06 5.117510 0.0785065
GTF2H4 37 0.8668279 0.6436612 9.00e-06 5.047485 0.0922334
MOBKL2A 19 1.4841498 1.4906497 1.14e-05 4.941419 0.1177368
BAT5 36 1.2842811 1.5412238 1.21e-05 4.918559 0.1240880
SUPT6H 18 1.1921515 1.0286504 1.53e-05 4.816480 0.1569519
SDF2 18 1.1921515 1.0286504 1.53e-05 4.816480 0.1569519
NEU1 44 1.1231732 1.1072696 1.76e-05 4.754234 0.1811038
GAS5 21 1.1682993 1.3449686 1.81e-05 4.741846 0.1863260
ZBTB37 21 1.1682993 1.3449686 1.81e-05 4.741846 0.1863260
CLASP1 23 1.2846301 1.2664006 2.10e-05 4.678177 0.2157040
SLC3A2 29 0.9246752 0.5651746 2.11e-05 4.674721 0.2174063
ANKRD11 27 1.1201580 0.8831639 3.02e-05 4.519498 0.3107800
TUBB 27 0.9258691 0.8629931 3.02e-05 4.519498 0.3107800
KLC4 16 1.9920173 2.1731240 3.05e-05 4.515450 0.3136292
HOXA4 16 1.3396100 1.3790624 3.05e-05 4.515450 0.3136292
PRRT1 20 -1.0570225 -1.3187925 3.62e-05 4.440816 0.3723621
ABCF1 24 1.5554173 1.5026175 3.66e-05 4.436552 0.3760002
JMJD6 19 1.4301622 1.1532646 3.81e-05 4.418540 0.3918839
C17orf95 19 1.4301622 1.1532646 3.81e-05 4.418540 0.3918839
FKBP11 18 1.5642747 1.7745641 3.81e-05 4.418540 0.3918839
C6orf48 42 0.9311312 0.6285010 3.84e-05 4.415164 0.3948267
MICA 40 0.9249490 0.9824856 4.10e-05 4.387341 0.4209077
SNORD95 21 1.6458351 1.7951432 4.10e-05 4.387131 0.4210701
B9D2 21 1.4673615 1.4784295 4.10e-05 4.387131 0.4210701
LTB 28 1.1795730 1.1287674 4.21e-05 4.375608 0.4323083
UBE2V1 19 1.5546075 1.5404940 5.34e-05 4.272412 0.5482101
RNASEK 18 1.5075154 1.1314396 5.34e-05 4.272412 0.5482101 
gmea_volc(res)

gmea_barplot(res)

dmscore <- data.frame( res$median * res$sig)
rownames(dmscore) <- rownames(res)
colnames(dmscore) <- "metric"
mres <- mitch_calc(x=dmscore, genesets=genesets,priority="effect")
## Note: Enrichments with large effect sizes may not be
##             statistically significant.
head(mres$enrichment_result,20) %>%  kbl(caption = "Top enriched gene sets with GMEA-Mitch (promoter only)") %>% kable_paper("hover", full_width = F)
Top enriched gene sets with GMEA-Mitch (promoter only)
set setSize pANOVA s.dist p.adjustANOVA
1152 VLDLR internalisation and degradation 11 0.0015811 0.5500079 0.0137563
409 HSF1 activation 21 0.0000544 0.5086938 0.0012225
893 SARS-CoV-2 modulates host translation machinery 38 0.0000001 0.5071482 0.0000025
69 Attenuation phase 19 0.0006139 0.4538873 0.0067134
292 Eukaryotic Translation Elongation 72 0.0000000 0.4382479 0.0000000
683 Peptide chain elongation 69 0.0000000 0.4360205 0.0000001
294 Eukaryotic Translation Termination 72 0.0000000 0.4224007 0.0000001
726 Processive synthesis on the lagging strand 13 0.0085961 0.4208663 0.0569254
329 Formation of the ternary complex, and subsequently, the 43S complex 40 0.0000044 0.4195001 0.0001555
236 Diseases associated with glycosylation precursor biosynthesis 15 0.0053562 0.4152586 0.0389302
325 Formation of a pool of free 40S subunits 78 0.0000000 0.4132790 0.0000001
595 NOTCH2 Activation and Transmission of Signal to the Nucleus 12 0.0137385 0.4107530 0.0791127
922 Selenocysteine synthesis 70 0.0000000 0.4102941 0.0000002
1157 Viral mRNA Translation 69 0.0000000 0.4080876 0.0000003
905 STING mediated induction of host immune responses 10 0.0257618 0.4071533 0.1293073
866 Removal of the Flap Intermediate 12 0.0160099 0.4015306 0.0867447
596 NOTCH3 Activation and Transmission of Signal to the Nucleus 15 0.0070889 0.4015213 0.0491575
410 HSF1-dependent transactivation 25 0.0005420 0.3996967 0.0060948
775 RIP-mediated NFkB activation via ZBP1 13 0.0129269 0.3981404 0.0757178
584 Myogenesis 13 0.0143485 -0.3921583 0.0818346 
#mitch_report(mres,outfile="gmeapr_mitch_nat_vs_GIFT.html",overwrite=FALSE)
rm(iui_vs_fx)

Session Information

For reproducibility.

sessionInfo()
## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 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_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] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] tictoc_1.0.1                                       
##  [2] kableExtra_1.3.4                                   
##  [3] dplyr_1.0.9                                        
##  [4] mitch_1.8.0                                        
##  [5] ENmix_1.32.0                                       
##  [6] doParallel_1.0.17                                  
##  [7] qqman_0.1.8                                        
##  [8] RCircos_1.2.2                                      
##  [9] beeswarm_0.4.0                                     
## [10] forestplot_2.0.1                                   
## [11] checkmate_2.1.0                                    
## [12] magrittr_2.0.3                                     
## [13] reshape2_1.4.4                                     
## [14] gplots_3.1.3                                       
## [15] eulerr_6.1.1                                       
## [16] GEOquery_2.64.2                                    
## [17] RColorBrewer_1.1-3                                 
## [18] IlluminaHumanMethylation450kmanifest_0.4.0         
## [19] topconfects_1.12.0                                 
## [20] DMRcatedata_2.14.0                                 
## [21] ExperimentHub_2.4.0                                
## [22] AnnotationHub_3.4.0                                
## [23] BiocFileCache_2.4.0                                
## [24] dbplyr_2.1.1                                       
## [25] DMRcate_2.10.0                                     
## [26] limma_3.52.1                                       
## [27] missMethyl_1.30.0                                  
## [28] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
## [29] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 
## [30] minfi_1.42.0                                       
## [31] bumphunter_1.38.0                                  
## [32] locfit_1.5-9.5                                     
## [33] iterators_1.0.14                                   
## [34] foreach_1.5.2                                      
## [35] Biostrings_2.64.0                                  
## [36] XVector_0.36.0                                     
## [37] SummarizedExperiment_1.26.1                        
## [38] Biobase_2.56.0                                     
## [39] MatrixGenerics_1.8.0                               
## [40] matrixStats_0.62.0                                 
## [41] GenomicRanges_1.48.0                               
## [42] GenomeInfoDb_1.32.2                                
## [43] IRanges_2.30.0                                     
## [44] S4Vectors_0.34.0                                   
## [45] BiocGenerics_0.42.0                                
## [46] R.utils_2.11.0                                     
## [47] R.oo_1.24.0                                        
## [48] R.methodsS3_1.8.1                                  
## [49] plyr_1.8.7                                         
## 
## loaded via a namespace (and not attached):
##   [1] rappdirs_0.3.3                rtracklayer_1.56.0           
##   [3] GGally_2.1.2                  tidyr_1.2.0                  
##   [5] ggplot2_3.3.6                 bit64_4.0.5                  
##   [7] knitr_1.39                    DelayedArray_0.22.0          
##   [9] data.table_1.14.2             rpart_4.1.16                 
##  [11] KEGGREST_1.36.0               RCurl_1.98-1.6               
##  [13] AnnotationFilter_1.20.0       generics_0.1.2               
##  [15] GenomicFeatures_1.48.1        preprocessCore_1.58.0        
##  [17] RSQLite_2.2.14                bit_4.0.4                    
##  [19] tzdb_0.3.0                    webshot_0.5.3                
##  [21] xml2_1.3.3                    httpuv_1.6.5                 
##  [23] assertthat_0.2.1              xfun_0.31                    
##  [25] hms_1.1.1                     jquerylib_0.1.4              
##  [27] evaluate_0.15                 promises_1.2.0.1             
##  [29] fansi_1.0.3                   restfulr_0.0.13              
##  [31] scrime_1.3.5                  progress_1.2.2               
##  [33] caTools_1.18.2                readxl_1.4.0                 
##  [35] DBI_1.1.2                     geneplotter_1.74.0           
##  [37] htmlwidgets_1.5.4             reshape_0.8.9                
##  [39] purrr_0.3.4                   ellipsis_0.3.2               
##  [41] backports_1.4.1               permute_0.9-7                
##  [43] calibrate_1.7.7               annotate_1.74.0              
##  [45] biomaRt_2.52.0                sparseMatrixStats_1.8.0      
##  [47] vctrs_0.4.1                   ensembldb_2.20.1             
##  [49] withr_2.5.0                   cachem_1.0.6                 
##  [51] Gviz_1.40.1                   BSgenome_1.64.0              
##  [53] GenomicAlignments_1.32.0      prettyunits_1.1.1            
##  [55] mclust_5.4.9                  svglite_2.1.0                
##  [57] cluster_2.1.3                 RPMM_1.25                    
##  [59] lazyeval_0.2.2                crayon_1.5.1                 
##  [61] genefilter_1.78.0             labeling_0.4.2               
##  [63] edgeR_3.38.1                  pkgconfig_2.0.3              
##  [65] nlme_3.1-157                  ProtGenerics_1.28.0          
##  [67] nnet_7.3-17                   rlang_1.0.2                  
##  [69] lifecycle_1.0.1               filelock_1.0.2               
##  [71] dichromat_2.0-0.1             polyclip_1.10-0              
##  [73] cellranger_1.1.0              rngtools_1.5.2               
##  [75] base64_2.0                    Matrix_1.4-1                 
##  [77] Rhdf5lib_1.18.2               base64enc_0.1-3              
##  [79] viridisLite_0.4.0             png_0.1-7                    
##  [81] rjson_0.2.21                  bitops_1.0-7                 
##  [83] KernSmooth_2.23-20            rhdf5filters_1.8.0           
##  [85] blob_1.2.3                    DelayedMatrixStats_1.18.0    
##  [87] doRNG_1.8.2                   stringr_1.4.0                
##  [89] nor1mix_1.3-0                 readr_2.1.2                  
##  [91] jpeg_0.1-9                    scales_1.2.0                 
##  [93] memoise_2.0.1                 zlibbioc_1.42.0              
##  [95] compiler_4.2.0                BiocIO_1.6.0                 
##  [97] illuminaio_0.38.0             Rsamtools_2.12.0             
##  [99] cli_3.3.0                     DSS_2.44.0                   
## [101] htmlTable_2.4.0               Formula_1.2-4                
## [103] MASS_7.3-57                   tidyselect_1.1.2             
## [105] stringi_1.7.6                 highr_0.9                    
## [107] yaml_2.3.5                    askpass_1.1                  
## [109] latticeExtra_0.6-29           sass_0.4.1                   
## [111] VariantAnnotation_1.42.1      tools_4.2.0                  
## [113] rstudioapi_0.13               foreign_0.8-82               
## [115] bsseq_1.32.0                  gridExtra_2.3                
## [117] farver_2.1.0                  digest_0.6.29                
## [119] BiocManager_1.30.17           shiny_1.7.1                  
## [121] quadprog_1.5-8                Rcpp_1.0.8.3                 
## [123] siggenes_1.70.0               BiocVersion_3.15.2           
## [125] later_1.3.0                   org.Hs.eg.db_3.15.0          
## [127] httr_1.4.3                    AnnotationDbi_1.58.0         
## [129] biovizBase_1.44.0             colorspace_2.0-3             
## [131] rvest_1.0.2                   polylabelr_0.2.0             
## [133] XML_3.99-0.9                  splines_4.2.0                
## [135] statmod_1.4.36                multtest_2.52.0              
## [137] systemfonts_1.0.4             xtable_1.8-4                 
## [139] jsonlite_1.8.0                dynamicTreeCut_1.63-1        
## [141] R6_2.5.1                      echarts4r_0.4.3              
## [143] Hmisc_4.7-0                   pillar_1.7.0                 
## [145] htmltools_0.5.2               mime_0.12                    
## [147] glue_1.6.2                    fastmap_1.1.0                
## [149] BiocParallel_1.30.2           interactiveDisplayBase_1.34.0
## [151] beanplot_1.3.1                codetools_0.2-18             
## [153] utf8_1.2.2                    lattice_0.20-45              
## [155] bslib_0.3.1                   tibble_3.1.7                 
## [157] curl_4.3.2                    gtools_3.9.2                 
## [159] openssl_2.0.1                 survival_3.3-1               
## [161] rmarkdown_2.14                munsell_0.5.0                
## [163] rhdf5_2.40.0                  GenomeInfoDbData_1.2.8       
## [165] HDF5Array_1.24.0              impute_1.70.0                
## [167] gtable_0.3.0