PADDI enrichment analysis
Mark Ziemann
2026-06-02
Introduction
Let’s do some enrichment analysis.
suppressPackageStartupMessages({
library("gplots")
library("reshape2")
library("WGCNA")
library("dplyr")
library("DESeq2")
library("mitch")
library("MASS")
library("kableExtra")
library("ggplot2")
library("eulerr")
library("DT")
library("xlsx")
library("RhpcBLASctl")
})
load("qc.Rds")
RhpcBLASctl::blas_set_num_threads(1)
#knitr::opts_chunk$set(dev = 'svg') # set output device to svgLoad GO gene sets
#reactome <- mitch::gmt_import("ReactomePathways_30oct24.gmt")
go <- mitch::gmt_import("c5.go.v2024.1.Hs.symbols.gmt")
names(go) <- gsub("_"," ",names(go))Gene table
gt <- read.table("../ref/gencode.v38.genetable.tsv")
rownames(gt) <- paste(gt[,1],gt[,2])
gt[,1] <- rownames(gt)Individual contrast analysis unstratified
Start with GO gene sets
Firstly we do the unstratified contrasts.
- crp_t0_adj
- crp_eos_adj
- crp_pod1_adj
- avb_t0_adj
- avb_eos_adj
- avb_pod1_adj
de <- crp_t0_adj
myname <- "crp_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 8723 | GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | 5 | 0.0009784 | -0.8512326 | 0.0182220 |
| 1440 | GOBP GANGLIOSIDE CATABOLIC PROCESS | 5 | 0.0011658 | -0.8384450 | 0.0207997 |
| 9082 | GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | 5 | 0.0012741 | -0.8318957 | 0.0222233 |
| 182 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0014691 | -0.8213035 | 0.0247472 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0014691 | -0.8213035 | 0.0247472 |
| 3150 | GOBP NEUTROPHIL CLEARANCE | 6 | 0.0012734 | -0.7594676 | 0.0222233 |
| 8488 | GOMF LIPOPOLYSACCHARIDE IMMUNE RECEPTOR ACTIVITY | 6 | 0.0021042 | -0.7248750 | 0.0326536 |
| 4418 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0000734 | -0.6902878 | 0.0023754 |
| 9021 | GOMF RETROMER COMPLEX BINDING | 9 | 0.0003677 | -0.6856401 | 0.0086147 |
| 189 | GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | 7 | 0.0017315 | -0.6837057 | 0.0280058 |
| 6322 | GOBP SPHINGOMYELIN BIOSYNTHETIC PROCESS | 10 | 0.0001968 | -0.6798170 | 0.0051171 |
| 5735 | GOBP REGULATION OF TRANSLATION INITIATION IN RESPONSE TO ENDOPLASMIC RETICULUM STRESS | 8 | 0.0012597 | -0.6583798 | 0.0220548 |
| 846 | GOBP COPPER ION TRANSMEMBRANE TRANSPORT | 7 | 0.0026283 | -0.6565103 | 0.0386959 |
| 8038 | GOMF COPPER ION TRANSMEMBRANE TRANSPORTER ACTIVITY | 7 | 0.0026283 | -0.6565103 | 0.0386959 |
| 8746 | GOMF OXIDOREDUCTASE ACTIVITY ACTING ON A SULFUR GROUP OF DONORS NAD P AS ACCEPTOR | 11 | 0.0002091 | -0.6455381 | 0.0053264 |
| 9318 | GOMF UNMETHYLATED CPG BINDING | 10 | 0.0004429 | 0.6415005 | 0.0100006 |
| 1521 | GOBP GLYCOLIPID CATABOLIC PROCESS | 16 | 0.0000097 | -0.6386703 | 0.0004356 |
| 264 | GOBP AUTOPHAGIC CELL DEATH | 8 | 0.0018456 | -0.6357264 | 0.0294453 |
| 7329 | GOCC MYOSIN FILAMENT | 12 | 0.0001846 | 0.6233034 | 0.0049742 |
| 7390 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0001087 | -0.6198648 | 0.0032154 |
| 446 | GOBP CARDIAC NEURAL CREST CELL DIFFERENTIATION INVOLVED IN HEART DEVELOPMENT | 9 | 0.0013388 | -0.6173805 | 0.0231352 |
| 1444 | GOBP GASTRO INTESTINAL SYSTEM SMOOTH MUSCLE CONTRACTION | 9 | 0.0014235 | -0.6139752 | 0.0241971 |
| 9321 | GOMF VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 BINDING | 8 | 0.0027661 | -0.6109459 | 0.0399699 |
| 2905 | GOBP NEGATIVE REGULATION OF PROTEIN EXIT FROM ENDOPLASMIC RETICULUM | 10 | 0.0009083 | -0.6057823 | 0.0172255 |
| 8306 | GOMF HAPTOGLOBIN BINDING | 8 | 0.0030508 | 0.6048166 | 0.0429699 |
| 1774 | GOBP INTERLEUKIN 33 MEDIATED SIGNALING PATHWAY | 8 | 0.0031017 | -0.6037760 | 0.0434103 |
| 1961 | GOBP LOCOMOTION INVOLVED IN LOCOMOTORY BEHAVIOR | 10 | 0.0011402 | -0.5940897 | 0.0205790 |
| 7620 | GOCC SPECTRIN ASSOCIATED CYTOSKELETON | 8 | 0.0036754 | 0.5930153 | 0.0497274 |
| 4362 | GOBP PROGESTERONE RECEPTOR SIGNALING PATHWAY | 9 | 0.0021039 | -0.5919064 | 0.0326536 |
| 872 | GOBP CRD MEDIATED MRNA STABILIZATION | 10 | 0.0012884 | -0.5877219 | 0.0224310 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_t0_adj_mitchreport.rds ".##
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## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb56758e96.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_eos_adj
myname <- "crp_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 183 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0002472 | -0.9463490 | 0.0044771 |
| 8512 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0002472 | -0.9463490 | 0.0044771 |
| 8491 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0002762 | -0.9390015 | 0.0049122 |
| 7550 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0006205 | -0.8837137 | 0.0094346 |
| 7048 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 53 | 0.0000000 | -0.8614954 | 0.0000000 |
| 257 | GOBP ATRIOVENTRICULAR NODE DEVELOPMENT | 5 | 0.0008932 | 0.8578158 | 0.0122641 |
| 8838 | GOMF PEROXIREDOXIN ACTIVITY | 8 | 0.0000390 | -0.8397072 | 0.0009089 |
| 7331 | GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 10 | 0.0000047 | -0.8361272 | 0.0001439 |
| 7125 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | 7 | 0.0001316 | -0.8343683 | 0.0026788 |
| 7551 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 13 | 0.0000002 | -0.8335864 | 0.0000086 |
| 7795 | GOMF 5S RRNA BINDING | 9 | 0.0000156 | -0.8313173 | 0.0004193 |
| 8723 | GOMF NUCLEASE INHIBITOR ACTIVITY | 6 | 0.0005076 | -0.8195183 | 0.0080161 |
| 6771 | GOBP VIRAL TRANSLATIONAL TERMINATION REINITIATION | 5 | 0.0015367 | -0.8179322 | 0.0188444 |
| 9326 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0000223 | -0.8161184 | 0.0005687 |
| 9186 | GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | 158 | 0.0000000 | -0.8122797 | 0.0000000 |
| 7264 | GOCC LARGE RIBOSOMAL SUBUNIT | 110 | 0.0000000 | -0.8076493 | 0.0000000 |
| 7428 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000005 | -0.8075069 | 0.0000184 |
| 7275 | GOCC LSM1 7 PAT1 COMPLEX | 5 | 0.0019825 | -0.7986178 | 0.0228247 |
| 4434 | GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 6 | 0.0007255 | 0.7966626 | 0.0106018 |
| 7699 | GOCC TOM COMPLEX | 7 | 0.0002815 | -0.7925739 | 0.0049827 |
| 9237 | GOMF THIOREDOXIN DEPENDENT PEROXIREDOXIN ACTIVITY | 6 | 0.0007728 | -0.7925704 | 0.0110506 |
| 2809 | GOBP NEGATIVE REGULATION OF MESENCHYMAL CELL PROLIFERATION | 5 | 0.0021516 | -0.7923252 | 0.0242016 |
| 7333 | GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | 32 | 0.0000000 | -0.7910275 | 0.0000000 |
| 7581 | GOCC RIBOSOMAL SUBUNIT | 182 | 0.0000000 | -0.7898508 | 0.0000000 |
| 3799 | GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | 10 | 0.0000170 | -0.7853563 | 0.0004501 |
| 6895 | GOCC BOX C D RNP COMPLEX | 5 | 0.0024484 | -0.7823043 | 0.0266329 |
| 6235 | GOBP SEQUESTERING OF IRON ION | 5 | 0.0024501 | -0.7822497 | 0.0266329 |
| 7537 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000193 | -0.7802447 | 0.0005049 |
| 7549 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | 21 | 0.0000000 | -0.7777734 | 0.0000000 |
| 8755 | GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | 5 | 0.0026004 | -0.7775939 | 0.0277526 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_eos_adj_mitchreport.rds ".##
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## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb6f324fb6.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_pod1_adj
myname <- "crp_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 181 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0001945 | -0.9620858 | 0.0030418 |
| 8428 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0001945 | -0.9620858 | 0.0030418 |
| 2016 | GOBP L LEUCINE CATABOLIC PROCESS | 5 | 0.0008973 | -0.8574925 | 0.0102543 |
| 8370 | GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | 5 | 0.0009515 | 0.8532568 | 0.0107155 |
| 7671 | GOCC UBIQUINONE BIOSYNTHESIS COMPLEX | 6 | 0.0005284 | -0.8169781 | 0.0067713 |
| 1841 | GOBP ISG15 PROTEIN CONJUGATION | 6 | 0.0005373 | -0.8159113 | 0.0068672 |
| 5864 | GOBP RESPONSE TO CORTISOL | 5 | 0.0019180 | 0.8011483 | 0.0184093 |
| 3246 | GOBP N ACYLPHOSPHATIDYLETHANOLAMINE METABOLIC PROCESS | 6 | 0.0007764 | -0.7922687 | 0.0092241 |
| 7067 | GOCC EXTRINSIC COMPONENT OF MITOCHONDRIAL INNER MEMBRANE | 6 | 0.0007890 | -0.7912176 | 0.0093502 |
| 8601 | GOMF NERVE GROWTH FACTOR BINDING | 6 | 0.0009133 | 0.7816319 | 0.0103991 |
| 7533 | GOCC SARCOPLASMIC RETICULUM LUMEN | 5 | 0.0026122 | 0.7772402 | 0.0232697 |
| 7621 | GOCC TIM22 MITOCHONDRIAL IMPORT INNER MEMBRANE INSERTION COMPLEX | 7 | 0.0003786 | -0.7757292 | 0.0052579 |
| 4896 | GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 8 | 0.0001571 | 0.7715698 | 0.0025559 |
| 4884 | GOBP REGULATION OF CILIUM BEAT FREQUENCY INVOLVED IN CILIARY MOTILITY | 7 | 0.0004351 | -0.7677143 | 0.0058670 |
| 8611 | GOMF NEUROTROPHIN BINDING | 7 | 0.0004797 | 0.7620392 | 0.0063223 |
| 6706 | GOBP VIRAL TRANSLATIONAL TERMINATION REINITIATION | 5 | 0.0032873 | -0.7590361 | 0.0276900 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0002185 | 0.7546364 | 0.0033832 |
| 1200 | GOBP EOSINOPHIL DIFFERENTIATION | 5 | 0.0037032 | 0.7494541 | 0.0302000 |
| 8407 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0037075 | -0.7493599 | 0.0302000 |
| 5025 | GOBP REGULATION OF FEVER GENERATION | 8 | 0.0002591 | 0.7457519 | 0.0038890 |
| 6137 | GOBP SA NODE CELL TO ATRIAL CARDIAC MUSCLE CELL SIGNALING | 5 | 0.0042908 | 0.7374623 | 0.0332718 |
| 7055 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | 7 | 0.0008381 | -0.7288901 | 0.0097827 |
| 828 | GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 11 | 0.0000292 | 0.7276750 | 0.0006678 |
| 5896 | GOBP RESPONSE TO GRAM POSITIVE BACTERIUM | 5 | 0.0048473 | 0.7274096 | 0.0363487 |
| 6136 | GOBP SA NODE CELL TO ATRIAL CARDIAC MUSCLE CELL COMMUNICATION | 6 | 0.0020510 | 0.7266751 | 0.0192871 |
| 8265 | GOMF HEMOGLOBIN BINDING | 7 | 0.0008919 | 0.7251113 | 0.0102182 |
| 6829 | GOCC BOX C D RNP COMPLEX | 5 | 0.0051412 | -0.7225151 | 0.0379100 |
| 1484 | GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | 5 | 0.0052750 | -0.7203690 | 0.0386000 |
| 1098 | GOBP ECTODERMAL CELL DIFFERENTIATION | 6 | 0.0023221 | 0.7179210 | 0.0213402 |
| 6536 | GOBP TRNA SURVEILLANCE | 8 | 0.0004629 | -0.7147799 | 0.0061621 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_pod1_adj_mitchreport.rds ".##
##
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## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb3b575171.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEMulti-contrast enrichment analysis.
l1 <- list("crp_t0_adj"=crp_t0_adj,"crp_eos_adj"=crp_eos_adj,
"crp_pod1_adj"=crp_pod1_adj,"avb_t0_adj"=avb_t0_adj,
"avb_eos_adj"=avb_eos_adj,"avb_pod1_adj"=avb_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm1 <- mitch_calc(x=m1,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:9)]
rownames(top) <- top[,1]
top[,1] = NULL
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top GOs in multi enrichment analysis") |> kable_paper("hover", full_width = F)| s.crp_t0_adj | s.crp_eos_adj | s.crp_pod1_adj | s.avb_t0_adj | s.avb_eos_adj | s.avb_pod1_adj | |
|---|---|---|---|---|---|---|
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8195083 | -0.9451372 | -0.9618395 | -0.5592143 | -0.8345365 | -0.8455129 |
| GOMF LIPID ANTIGEN BINDING | -0.8195083 | -0.9451372 | -0.9618395 | -0.5592143 | -0.8345365 | -0.8455129 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.6124982 | -0.2161316 | 0.8558996 | -0.6377800 | -0.9498169 | 0.3278927 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.8496600 | -0.7733010 | 0.3138917 | 0.0277643 | -0.6641651 | 0.7488372 |
| GOMF UNMETHYLATED CPG BINDING | 0.6475882 | 0.6992579 | 0.3655504 | 0.8642755 | 0.5636761 | 0.0763200 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6812366 | -0.6814269 | -0.5741125 | -0.2839273 | -0.6884118 | -0.4528690 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | -0.2951158 | -0.2606649 | 0.7804347 | 0.4466353 | -0.4260142 | 0.9093737 |
| GOMF GUANYLATE CYCLASE ACTIVITY | -0.5090312 | -0.6607219 | 0.3116279 | -0.4642317 | -0.5910972 | 0.7271698 |
| GOCC SIGNAL PEPTIDASE COMPLEX | -0.7335616 | -0.7559899 | -0.3328007 | -0.3377467 | -0.4300471 | 0.5274076 |
| GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | -0.8301422 | -0.6714890 | 0.1712560 | -0.7428069 | -0.1596709 | 0.2062016 |
| GOBP SIALYLATION | 0.3437173 | 0.4938964 | 0.5696915 | 0.6637496 | 0.4600812 | 0.6473255 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.3886527 | -0.9377182 | -0.7479812 | -0.0977695 | -0.1265135 | -0.3362439 |
| GOMF NEUROTROPHIN BINDING | -0.1025786 | -0.2528215 | 0.7653678 | -0.4808765 | -0.7916494 | 0.4336674 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.8368384 | -0.6641461 | -0.3526038 | -0.5253151 | 0.0558425 | -0.3900224 |
| GOBP VIRAL TRANSLATIONAL TERMINATION REINITIATION | -0.2735816 | -0.8137252 | -0.7576640 | 0.0840348 | -0.2414705 | -0.5572740 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.1578522 | -0.1842798 | 0.7847903 | -0.4801833 | -0.7664320 | 0.4257744 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.4704400 | -0.8306914 | -0.7273722 | -0.1267946 | -0.2572380 | -0.3604213 |
| GOMF HEMOGLOBIN BINDING | 0.3354850 | 0.3375234 | 0.7282147 | 0.6389061 | 0.1136402 | 0.6857890 |
| GOMF PHOSPHATIDYLETHANOLAMINE FLIPPASE ACTIVITY | 0.3079374 | 0.6164931 | 0.6903029 | 0.4820374 | -0.1483902 | 0.6624911 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.2149878 | -0.5647135 | -0.0064048 | -0.6123847 | -0.9256001 | -0.1832018 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.3432893 | -0.7126098 | -0.7076160 | 0.0957386 | 0.4385681 | -0.5294873 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.2409173 | -0.8751282 | -0.0402310 | 0.1709462 | -0.7546051 | 0.4175098 |
| GOMF PROTEIN PHOSPHATASE 2B BINDING | 0.0594949 | 0.2991677 | 0.4860893 | 0.4945736 | 0.6330432 | 0.7859894 |
| GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | -0.6102463 | -0.7501070 | -0.2286462 | -0.3977374 | -0.1330457 | 0.6277900 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5152034 | 0.2092013 | -0.3362662 | -0.6812042 | -0.0696281 | -0.8103935 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.5645979 | -0.5993342 | -0.7188187 | 0.0256147 | 0.5512627 | -0.2090550 |
| GOCC BOX C D RNP COMPLEX | 0.0616446 | -0.7772768 | -0.7209302 | 0.0223047 | -0.1807676 | -0.5995054 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | -0.1202955 | 0.3730461 | 0.6816323 | 0.3878056 | 0.2459653 | 0.8213165 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.2252188 | 0.6751094 | 0.7736515 | -0.0418688 | -0.1560597 | 0.6020738 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | -0.1169829 | 0.3041328 | 0.6638988 | -0.2046417 | -0.6587055 | 0.6565749 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | -0.3607432 | -0.5272606 | 0.5447929 | 0.2691983 | -0.5830663 | 0.5760257 |
| GOBP REGULATION OF NITRIC OXIDE MEDIATED SIGNAL TRANSDUCTION | -0.3685262 | -0.5333619 | 0.5008513 | -0.4895515 | -0.7059590 | -0.1571979 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | -0.1038379 | 0.3929709 | 0.3946069 | -0.7768964 | -0.6404813 | -0.2717934 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | -0.4757126 | 0.4970477 | 0.4756311 | 0.4296042 | 0.2183183 | 0.6848106 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.6166838 | -0.8033647 | -0.0895197 | 0.1709186 | -0.4075836 | 0.4093329 |
| GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 0.5256531 | 0.5234245 | 0.2710447 | 0.6995685 | 0.0689315 | 0.5194021 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.1479949 | 0.5753770 | 0.7302351 | -0.0239803 | -0.0136963 | 0.7044514 |
| GOCC MHC CLASS II PROTEIN COMPLEX | 0.0425465 | -0.4504956 | -0.6705524 | 0.2886711 | 0.5916195 | -0.5404736 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.2550689 | -0.8757810 | -0.6899281 | -0.0976883 | -0.0089426 | -0.2354568 |
| GOCC TOM COMPLEX | -0.4091795 | -0.7891490 | -0.6323968 | -0.3025310 | -0.2649703 | -0.0614303 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | -0.5549320 | 0.0041219 | 0.4822918 | -0.0906497 | -0.3095850 | 0.8317638 |
| GOBP REGULATION OF MONOATOMIC ANION TRANSMEMBRANE TRANSPORT | 0.1604318 | 0.6618443 | 0.1336662 | 0.6289342 | 0.4798878 | 0.4720692 |
| GOMF RETROMER COMPLEX BINDING | -0.6824325 | -0.4221250 | 0.2937576 | -0.2050611 | -0.6599386 | 0.3404050 |
| GOCC ARP2 3 PROTEIN COMPLEX | -0.5179248 | -0.3225409 | 0.4729370 | -0.0001638 | -0.4788671 | 0.7026326 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | -0.6876630 | -0.2458105 | 0.4853631 | 0.0277774 | -0.4554017 | 0.5729725 |
| GOCC F ACTIN CAPPING PROTEIN COMPLEX | -0.3607066 | -0.2261457 | 0.6854629 | -0.1693970 | -0.3227382 | 0.7195583 |
| GOBP NEGATIVE REGULATION OF BLOOD VESSEL ENDOTHELIAL CELL PROLIFERATION INVOLVED IN SPROUTING ANGIOGENESIS | -0.1781614 | -0.3327056 | 0.6307795 | -0.5679460 | -0.6120226 | -0.2191183 |
| GOBP PEPTIDE ANTIGEN ASSEMBLY WITH MHC CLASS II PROTEIN COMPLEX | 0.0406726 | -0.4428041 | -0.6487704 | 0.2657246 | 0.5703071 | -0.5146405 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.3719997 | 0.0930435 | 0.7152890 | 0.1750690 | 0.0257935 | 0.7598846 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.4250440 | -0.5229562 | -0.8566224 | 0.0187854 | 0.2804109 | 0.0031864 |
mitch_report(res=mm1,outfile="multigo_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/multigo_all_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
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## 5/36
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## 12/36 [input_geneset_metrics1]
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## 16/36 [input_geneset_metrics3]
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## 21/36 [heatmap]## 22/36
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## 28/36
## 29/36 [detailed_geneset_reports1d]
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## 31/36 [detailed_geneset_reports2d]## 32/36
## 33/36 [network]
## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb4859a50d.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEThis might work better if we work on each timepoint separately.
l1 <- list("crp_t0_adj"=crp_t0_adj, "avb_t0_adj"=avb_t0_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top GOs in multi enrichment analysis at t0") |> kable_paper("hover", full_width = F)| s.crp_t0_adj | s.avb_t0_adj | |
|---|---|---|
| GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | -0.8318957 | -0.7391630 |
| GOMF UNMETHYLATED CPG BINDING | 0.6415005 | 0.8655993 |
| GOCC ATP BINDING CASSETTE ABC TRANSPORTER COMPLEX | 0.7081546 | 0.7853190 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8213035 | -0.5548868 |
| GOMF LIPID ANTIGEN BINDING | -0.8213035 | -0.5548868 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.8384450 | -0.5206952 |
| GOCC MPP7 DLG1 LIN7 COMPLEX | -0.6431008 | -0.6932083 |
| GOCC TORC1 COMPLEX | 0.5450665 | 0.7102238 |
| GOBP NOTOCHORD MORPHOGENESIS | 0.5957815 | 0.6518580 |
| GOMF HAPTOGLOBIN BINDING | 0.6048166 | 0.6358636 |
| GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 0.5195405 | 0.7026418 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.8512326 | 0.0334507 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5112361 | -0.6776284 |
| GOMF FATTY ACYL COA SYNTHASE ACTIVITY | -0.0991082 | -0.7903865 |
| GOCC HEMOGLOBIN COMPLEX | 0.5498994 | 0.5605581 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | -0.1110176 | -0.7738669 |
| GOBP MITOTIC SPINDLE ELONGATION | 0.2121406 | 0.7466490 |
| GOMF GABA A RECEPTOR ACTIVITY | 0.1665767 | -0.7553716 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.4688868 | 0.6095533 |
| GOBP LEUKOCYTE ADHESION TO ARTERIAL ENDOTHELIAL CELL | -0.0647153 | -0.7661102 |
| GOBP NEUTROPHIL CLEARANCE | -0.7594676 | -0.0741401 |
| GOMF LIPOPOLYSACCHARIDE IMMUNE RECEPTOR ACTIVITY | -0.7248750 | -0.2256678 |
| GOBP PROTEIN DEMETHYLATION | 0.2149897 | 0.7268093 |
| GOBP REGULATION OF TRANSLATION INITIATION IN RESPONSE TO ENDOPLASMIC RETICULUM STRESS | -0.6583798 | -0.3692594 |
| GOCC MYOSIN FILAMENT | 0.6233034 | 0.4184585 |
| GOMF SERINE TYPE EXOPEPTIDASE ACTIVITY | -0.5735316 | -0.4829552 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6837057 | -0.2798531 |
| GOCC NETWORK FORMING COLLAGEN TRIMER | -0.0551592 | -0.7359129 |
| GOBP TELOMERE MAINTENANCE VIA SEMI CONSERVATIVE REPLICATION | 0.2231828 | 0.6983161 |
| GOBP SPHINGOMYELIN BIOSYNTHETIC PROCESS | -0.6798170 | -0.2716102 |
| GOBP GASTRO INTESTINAL SYSTEM SMOOTH MUSCLE CONTRACTION | -0.6139752 | -0.3812726 |
| GOBP SPINDLE ELONGATION | 0.1563625 | 0.7052731 |
| GOBP REGULATION OF CDC42 PROTEIN SIGNAL TRANSDUCTION | -0.2932266 | 0.6580471 |
| GOBP POSITIVE REGULATION OF FEVER GENERATION | -0.2542783 | -0.6708594 |
| GOBP GLYCOLIPID CATABOLIC PROCESS | -0.6386703 | -0.3251293 |
| GOMF RETROMER COMPLEX BINDING | -0.6856401 | -0.1998435 |
| GOMF DNA TOPOISOMERASE ACTIVITY | 0.0779516 | 0.7076320 |
| GOBP NOTOCHORD DEVELOPMENT | 0.4574032 | 0.5418753 |
| GOBP PARTURITION | -0.5110247 | -0.4842818 |
| GOBP SPINDLE MIDZONE ASSEMBLY | 0.0588616 | 0.6988256 |
| GOBP BASE EXCISION REPAIR GAP FILLING | 0.2277505 | 0.6624137 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | -0.6902878 | 0.0336246 |
| GOBP MRNA 3 SPLICE SITE RECOGNITION | 0.0212526 | 0.6902061 |
| GOBP REGULATION OF FEVER GENERATION | -0.1812620 | -0.6601866 |
| GOBP REGULATION OF DNA TEMPLATED DNA REPLICATION INITIATION | 0.2438363 | 0.6396478 |
| GOCC GABA RECEPTOR COMPLEX | 0.2953256 | -0.6111568 |
| GOMF GABA RECEPTOR ACTIVITY | 0.2953256 | -0.6111568 |
| GOBP NEGATIVE REGULATION OF PROTEIN LOCALIZATION TO CELL SURFACE | -0.5050011 | -0.4427592 |
| GOMF SULFATIDE BINDING | -0.5304642 | 0.4107661 |
| GOMF ANKYRIN REPEAT BINDING | -0.0348518 | 0.6656300 |
mitch_report(res=mm1,outfile="multigo_t0_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/multigo_t0_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]
## 30/36
## 31/36 [detailed_geneset_reports2d]## 32/36
## 33/36 [network]
## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb471ff025.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEl1 <- list("crp_eos_adj"=crp_eos_adj, "avb_eos_adj"=avb_eos_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top GOs in multi enrichment analysis at EOS") |> kable_paper("hover", full_width = F)| s.crp_eos_adj | s.avb_eos_adj | |
|---|---|---|
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.9463490 | -0.8317905 |
| GOMF LIPID ANTIGEN BINDING | -0.9463490 | -0.8317905 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7775939 | -0.6581068 |
| GOBP REGULATION OF CALCIUM ION EXPORT ACROSS PLASMA MEMBRANE | -0.7517141 | -0.6733655 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.5292896 | -0.8568939 |
| GOBP ATRIOVENTRICULAR NODE DEVELOPMENT | 0.8578158 | 0.5096481 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX CIRCULATING | -0.6083114 | -0.7687369 |
| GOBP POSITIVE REGULATION OF SYNAPTIC VESICLE ENDOCYTOSIS | -0.5194326 | -0.8270619 |
| GOBP POSITIVE REGULATION OF SYNAPTIC VESICLE RECYCLING | -0.5775737 | -0.7865458 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.2197872 | -0.9491316 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6843787 | -0.6834953 |
| GOMF C PALMITOYLTRANSFERASE ACTIVITY | -0.4776212 | -0.8370828 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.3957543 | -0.8659902 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.9390015 | -0.1156679 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.7717092 | -0.5135894 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8837137 | -0.2706920 |
| GOMF NUCLEASE INHIBITOR ACTIVITY | -0.8195183 | -0.4086755 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.5323935 | -0.7320802 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | 0.1789579 | 0.8841866 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.8075069 | -0.4007795 |
| GOMF UNMETHYLATED CPG BINDING | 0.6967120 | 0.5711583 |
| GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 0.7966626 | -0.4051592 |
| GOMF 5S RRNA BINDING | -0.8313173 | -0.3025416 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8335864 | -0.2640142 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.8343683 | -0.2471028 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8361272 | -0.2236937 |
| GOCC ENDOPLASMIC RETICULUM PALMITOYLTRANSFERASE COMPLEX | -0.5337297 | -0.6767541 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8614954 | 0.0114604 |
| GOMF PEROXIREDOXIN ACTIVITY | -0.8397072 | -0.1768678 |
| GOBP ATRIAL CARDIAC MUSCLE TISSUE DEVELOPMENT | 0.2485791 | 0.8109247 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.7171979 | 0.4477637 |
| GOCC TOM COMPLEX | -0.7925739 | -0.2559242 |
| GOCC INTRACILIARY TRANSPORT PARTICLE A | 0.2346983 | 0.7911987 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.6024007 | 0.5604438 |
| GOCC COLLAGEN TYPE IV TRIMER | 0.3771756 | -0.7287988 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | -0.7705124 | -0.2743689 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.8161184 | -0.0134303 |
| GOBP THYROID HORMONE TRANSPORT | -0.6597724 | -0.4796939 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.8122797 | -0.0204429 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7777734 | -0.2246446 |
| GOCC LARGE RIBOSOMAL SUBUNIT | -0.8076493 | -0.0531018 |
| GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | -0.7853563 | -0.1678021 |
| GOCC MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX III | -0.7597101 | -0.2517346 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 0.4488549 | -0.6594371 |
| GOBP PROTEIN LOCALIZATION TO CENP A CONTAINING CHROMATIN | -0.6379364 | -0.4777020 |
| GOMF THIOREDOXIN DEPENDENT PEROXIREDOXIN ACTIVITY | -0.7925704 | -0.0766001 |
| GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | -0.7910275 | -0.0641018 |
| GOCC RIBOSOMAL SUBUNIT | -0.7898508 | -0.0393130 |
| GOCC RESPIRATORY CHAIN COMPLEX IV | -0.7185313 | -0.3236134 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | -0.5336547 | -0.5782410 |
mitch_report(res=mm1,outfile="multigo_eos_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/multigo_eos_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb405525f5.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEl1 <- list("crp_pod1_adj"=crp_pod1_adj, "avb_pod1_adj"=avb_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mm1 <- mitch_calc(x=m1,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:5)]
rownames(top) <- top[,1]
top[,1] = NULL
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none", margins = c(6,25), cexRow=0.6, cexCol=0.8 )
as.matrix(top) |> kbl(caption="Top GOs in multi enrichment analysis at POD1") |> kable_paper("hover", full_width = F)| s.crp_pod1_adj | s.avb_pod1_adj | |
|---|---|---|
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.9620858 | -0.8456137 |
| GOMF LIPID ANTIGEN BINDING | -0.9620858 | -0.8456137 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | 0.7772402 | 0.9094691 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 0.6787625 | 0.8214493 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.7127124 | 0.7600132 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.7276750 | 0.7045048 |
| GOMF HEMOGLOBIN BINDING | 0.7251113 | 0.6859106 |
| GOCC F ACTIN CAPPING PROTEIN COMPLEX | 0.6820376 | 0.7195842 |
| GOBP N ACYLPHOSPHATIDYLETHANOLAMINE METABOLIC PROCESS | -0.7922687 | -0.5935740 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.7715698 | 0.6020828 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.4787029 | 0.8318978 |
| GOBP CHROMOSOME MOVEMENT TOWARDS SPINDLE POLE | 0.5547136 | 0.7788080 |
| GOMF INHIBITORY MHC CLASS I RECEPTOR ACTIVITY | 0.6102495 | 0.7354201 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | 0.8532568 | 0.3278614 |
| GOBP MEIOTIC CYTOKINESIS | 0.4106619 | 0.8011798 |
| GOBP NEGATIVE REGULATION OF DELAYED RECTIFIER POTASSIUM CHANNEL ACTIVITY | 0.6183214 | 0.6537432 |
| GOBP REGULATION OF CILIUM BEAT FREQUENCY INVOLVED IN CILIARY MOTILITY | -0.7677143 | -0.4675031 |
| GOMF NERVE GROWTH FACTOR BINDING | 0.7816319 | 0.4258327 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | -0.3058458 | -0.8354648 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.7091354 | -0.5297846 |
| GOMF NEUROTROPHIN BINDING | 0.7620392 | 0.4337489 |
| GOCC UBIQUINONE BIOSYNTHESIS COMPLEX | -0.8169781 | -0.3055804 |
| GOBP DENDRITIC CELL APOPTOTIC PROCESS | 0.6378899 | 0.5913513 |
| GOCC MHC CLASS II PROTEIN COMPLEX | -0.6719779 | -0.5406033 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.8574925 | 0.0033321 |
| GOBP CELLULAR HYPOTONIC RESPONSE | 0.5707232 | 0.6396787 |
| GOBP PLASMA CELL DIFFERENTIATION | 0.7546364 | 0.3834314 |
| GOBP INTESTINAL CHOLESTEROL ABSORPTION | 0.6864850 | 0.4940263 |
| GOCC ARP2 3 PROTEIN COMPLEX | 0.4687964 | 0.7028808 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.4712147 | 0.6849155 |
| GOBP PEPTIDE ANTIGEN ASSEMBLY WITH MHC CLASS II PROTEIN COMPLEX | -0.6502862 | -0.5147740 |
| GOBP DETOXIFICATION OF INORGANIC COMPOUND | 0.5633523 | 0.6075593 |
| GOMF BETA 2 MICROGLOBULIN BINDING | -0.6712484 | -0.4852717 |
| GOBP ISG15 PROTEIN CONJUGATION | -0.8159113 | 0.1156242 |
| GOCC MHC PROTEIN COMPLEX | -0.6731614 | -0.4734400 |
| GOCC EXTRINSIC COMPONENT OF MITOCHONDRIAL INNER MEMBRANE | -0.7912176 | -0.2013618 |
| GOBP RESPONSE TO CORTISOL | 0.8011483 | 0.1478163 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.7288901 | -0.3604981 |
| GOBP SA NODE CELL TO ATRIAL CARDIAC MUSCLE CELL COMMUNICATION | 0.7266751 | 0.3585134 |
| GOCC TIM22 MITOCHONDRIAL IMPORT INNER MEMBRANE INSERTION COMPLEX | -0.7757292 | -0.1784538 |
| GOCC CYTOLYTIC GRANULE | 0.4785671 | 0.6330672 |
| GOMF GLUCOSE BINDING | 0.6274448 | 0.4856417 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | 0.5418682 | 0.5760800 |
| GOBP NEGATIVE REGULATION OF T CELL MEDIATED CYTOTOXICITY | 0.5268416 | 0.5853261 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | -0.2465809 | 0.7362327 |
| GOBP LIPID DIGESTION | 0.6421543 | 0.4325126 |
| GOBP HYPOTONIC RESPONSE | 0.5281363 | 0.5653345 |
| GOBP U4 SNRNA 3 END PROCESSING | -0.7092375 | -0.3065780 |
| GOBP REGULATION OF CD8 POSITIVE ALPHA BETA T CELL DIFFERENTIATION | 0.6276418 | 0.4315251 |
| GOBP RRNA 3 END PROCESSING | -0.6953443 | -0.3106435 |
mitch_report(res=mm1,outfile="multigo_eos_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/multigo_eos_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
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## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbbf375318.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEIndividual contrast analysis stratified
- crp_t0_a_adj
- crp_t0_b_adj
- crp_eos_a_adj
- crp_eos_b_adj
- crp_pod1_a_adj
- crp_pod1_b_adj
- avb_crplo_t0_adj
- avb_crphi_t0_adj
- avb_crplo_eos_adj
- avb_crphi_eos_adj
- avb_crplo_pod1_adj
- avb_crphi_pod1_adj
de <- crp_t0_a_adj
myname <- "crp_t0_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 182 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0001523 | -0.9778642 | 0.0017518 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0001523 | -0.9778642 | 0.0017518 |
| 2070 | GOBP MAINTENANCE OF PROTEIN LOCATION IN MITOCHONDRION | 5 | 0.0003747 | -0.9185182 | 0.0038408 |
| 8458 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0004960 | -0.8993094 | 0.0048609 |
| 7513 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0009129 | -0.8562451 | 0.0080977 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0001251 | -0.8370894 | 0.0014660 |
| 189 | GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | 7 | 0.0001266 | -0.8364491 | 0.0014800 |
| 7294 | GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 10 | 0.0000058 | -0.8278774 | 0.0000981 |
| 7012 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 52 | 0.0000000 | -0.8206756 | 0.0000000 |
| 2203 | GOBP METHYLGLYOXAL METABOLIC PROCESS | 6 | 0.0005348 | -0.8162123 | 0.0051597 |
| 6205 | GOBP SEQUESTERING OF IRON ION | 5 | 0.0016199 | -0.8139675 | 0.0129883 |
| 7500 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000116 | -0.8007136 | 0.0001827 |
| 4988 | GOBP REGULATION OF ELECTRON TRANSFER ACTIVITY | 5 | 0.0020449 | -0.7962406 | 0.0157089 |
| 1522 | GOBP GLYCOLIPID TRANSPORT | 8 | 0.0001003 | -0.7940490 | 0.0012073 |
| 8723 | GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | 5 | 0.0021995 | -0.7906243 | 0.0167455 |
| 8228 | GOMF GABA A RECEPTOR ACTIVITY | 5 | 0.0022241 | 0.7897645 | 0.0168641 |
| 8429 | GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | 6 | 0.0009551 | -0.7786773 | 0.0083846 |
| 8901 | GOMF PORIN ACTIVITY | 6 | 0.0009593 | -0.7783876 | 0.0083980 |
| 7390 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000012 | -0.7767024 | 0.0000250 |
| 7814 | GOMF ADP RIBOSE DIPHOSPHATASE ACTIVITY | 6 | 0.0009908 | -0.7762532 | 0.0086086 |
| 7711 | GOCC U7 SNRNP | 7 | 0.0003780 | -0.7758117 | 0.0038668 |
| 2252 | GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | 14 | 0.0000006 | -0.7705174 | 0.0000129 |
| 1849 | GOBP ISOCITRATE METABOLIC PROCESS | 6 | 0.0010825 | -0.7703683 | 0.0092846 |
| 96 | GOBP ALDEHYDE CATABOLIC PROCESS | 10 | 0.0000246 | -0.7702928 | 0.0003534 |
| 8990 | GOMF PROTON TRANSPORTING ATP SYNTHASE ACTIVITY ROTATIONAL MECHANISM | 16 | 0.0000001 | -0.7645683 | 0.0000031 |
| 7514 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 13 | 0.0000021 | -0.7598235 | 0.0000402 |
| 6206 | GOBP SEQUESTERING OF METAL ION | 8 | 0.0002027 | -0.7585079 | 0.0022449 |
| 8438 | GOMF ISOCITRATE DEHYDROGENASE NAD P PLUS ACTIVITY | 5 | 0.0033519 | -0.7574754 | 0.0233162 |
| 9294 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0000832 | -0.7573761 | 0.0010325 |
| 7512 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | 21 | 0.0000000 | -0.7549370 | 0.0000001 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_t0_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
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## 11/36
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## 13/36
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## 16/36 [input_geneset_metrics3]## 17/36
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## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb2fa1b5e9.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_t0_b_adj
myname <- "crp_t0_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 9304 | GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 5 | 0.0004544 | -0.9053464 | 0.0356999 |
| 4996 | GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 6 | 0.0005571 | -0.8136206 | 0.0416643 |
| 1270 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0001931 | -0.8135271 | 0.0210458 |
| 3198 | GOBP NUCLEAR PORE ORGANIZATION | 15 | 0.0000044 | -0.6849173 | 0.0010996 |
| 3196 | GOBP NUCLEAR PORE COMPLEX ASSEMBLY | 11 | 0.0001520 | -0.6594538 | 0.0182949 |
| 7173 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0003295 | 0.6556999 | 0.0280057 |
| 4130 | GOBP POSITIVE REGULATION OF PROTEIN POLYUBIQUITINATION | 16 | 0.0000082 | -0.6437265 | 0.0018777 |
| 4418 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0002662 | -0.6348165 | 0.0239986 |
| 9025 | GOMF RIBOSOMAL LARGE SUBUNIT BINDING | 14 | 0.0002642 | -0.5630360 | 0.0239986 |
| 7333 | GOCC NADPH OXIDASE COMPLEX | 14 | 0.0004742 | 0.5394073 | 0.0369433 |
| 3168 | GOBP NLS BEARING PROTEIN IMPORT INTO NUCLEUS | 19 | 0.0002670 | -0.4830105 | 0.0239986 |
| 6506 | GOBP TOOTH MINERALIZATION | 19 | 0.0006463 | 0.4520111 | 0.0464816 |
| 1047 | GOBP DNA DOUBLE STRAND BREAK PROCESSING | 20 | 0.0005832 | -0.4441831 | 0.0432705 |
| 2301 | GOBP MITOTIC SISTER CHROMATID COHESION | 31 | 0.0001526 | -0.3929032 | 0.0182949 |
| 8239 | GOMF GDP BINDING | 63 | 0.0000047 | -0.3332533 | 0.0011677 |
| 8289 | GOMF G PROTEIN ACTIVITY | 41 | 0.0002568 | -0.3298711 | 0.0239986 |
| 2738 | GOBP NEGATIVE REGULATION OF INTRACELLULAR TRANSPORT | 39 | 0.0005203 | -0.3210690 | 0.0395483 |
| 4953 | GOBP REGULATION OF DENDRITIC SPINE DEVELOPMENT | 50 | 0.0002235 | -0.3016755 | 0.0219916 |
| 7189 | GOCC IMMUNOGLOBULIN COMPLEX | 112 | 0.0000000 | 0.2980817 | 0.0000334 |
| 196 | GOBP ANTIMICROBIAL HUMORAL IMMUNE RESPONSE MEDIATED BY ANTIMICROBIAL PEPTIDE | 53 | 0.0002796 | 0.2884777 | 0.0242042 |
| 7700 | GOCC T CELL RECEPTOR COMPLEX | 123 | 0.0000001 | 0.2837423 | 0.0000338 |
| 259 | GOBP ATTACHMENT OF SPINDLE MICROTUBULES TO KINETOCHORE | 52 | 0.0004014 | -0.2836719 | 0.0329197 |
| 8151 | GOMF DOUBLE STRANDED RNA BINDING | 70 | 0.0002166 | -0.2556265 | 0.0217751 |
| 7149 | GOCC GOLGI ASSOCIATED VESICLE | 80 | 0.0001611 | -0.2439881 | 0.0188249 |
| 197 | GOBP ANTIMICROBIAL HUMORAL RESPONSE | 83 | 0.0001455 | 0.2411580 | 0.0182949 |
| 7888 | GOMF ATP DEPENDENT ACTIVITY ACTING ON RNA | 72 | 0.0004884 | -0.2376365 | 0.0377330 |
| 9028 | GOMF RIBOSOME BINDING | 101 | 0.0000567 | -0.2317989 | 0.0093019 |
| 820 | GOBP COLLAGEN METABOLIC PROCESS | 76 | 0.0005062 | 0.2306815 | 0.0387928 |
| 4408 | GOBP PROTEIN DEUBIQUITINATION | 82 | 0.0003577 | -0.2279897 | 0.0298571 |
| 9302 | GOMF UBIQUITIN LIKE PROTEIN PEPTIDASE ACTIVITY | 106 | 0.0000655 | -0.2243821 | 0.0103776 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_t0_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb95fc437.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_eos_a_adj
myname <- "crp_eos_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 7331 | GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 10 | 0.0000029 | -0.8541271 | 0.0001708 |
| 7551 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 13 | 0.0000002 | -0.8318440 | 0.0000148 |
| 183 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0013553 | -0.8273165 | 0.0298447 |
| 8512 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0013553 | -0.8273165 | 0.0298447 |
| 8491 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0014395 | -0.8228244 | 0.0314047 |
| 7222 | GOCC IGE IMMUNOGLOBULIN COMPLEX | 5 | 0.0018881 | -0.8023461 | 0.0379287 |
| 7550 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0020753 | -0.7951078 | 0.0405582 |
| 4252 | GOBP POSITIVE REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY | 15 | 0.0000001 | -0.7832848 | 0.0000111 |
| 6601 | GOBP TRNA THIO MODIFICATION | 5 | 0.0024205 | -0.7831954 | 0.0451189 |
| 3799 | GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | 10 | 0.0000181 | -0.7827732 | 0.0008664 |
| 6593 | GOBP TRNA AMINOACYLATION FOR MITOCHONDRIAL PROTEIN TRANSLATION | 8 | 0.0001316 | -0.7805011 | 0.0046077 |
| 6806 | GOBP XMP METABOLIC PROCESS | 7 | 0.0004017 | -0.7723198 | 0.0117034 |
| 7699 | GOCC TOM COMPLEX | 7 | 0.0004349 | -0.7677337 | 0.0124771 |
| 8932 | GOMF PORIN ACTIVITY | 6 | 0.0011433 | -0.7667137 | 0.0264829 |
| 7549 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | 21 | 0.0000000 | -0.7663508 | 0.0000001 |
| 4817 | GOBP REGULATION OF CALCIUM IMPORT INTO THE MITOCHONDRION | 6 | 0.0015045 | -0.7481320 | 0.0322241 |
| 7223 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 11 | 0.0000194 | -0.7437528 | 0.0009221 |
| 6663 | GOBP U4 SNRNA 3 END PROCESSING | 8 | 0.0002734 | -0.7429403 | 0.0086925 |
| 3366 | GOBP OXALOACETATE METABOLIC PROCESS | 7 | 0.0006640 | -0.7428805 | 0.0176464 |
| 4530 | GOBP PROTEIN MATURATION BY 4FE 4S CLUSTER TRANSFER | 8 | 0.0002886 | -0.7400869 | 0.0090843 |
| 7249 | GOCC IRON SULFUR CLUSTER ASSEMBLY COMPLEX | 12 | 0.0000102 | -0.7357378 | 0.0005309 |
| 7428 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000044 | -0.7355590 | 0.0002484 |
| 1 | GOBP 2FE 2S CLUSTER ASSEMBLY | 11 | 0.0000250 | -0.7337060 | 0.0011518 |
| 2278 | GOBP MITOCHONDRIAL RIBOSOME ASSEMBLY | 12 | 0.0000115 | -0.7311138 | 0.0005849 |
| 9326 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0001530 | -0.7287151 | 0.0052576 |
| 7326 | GOCC MITOCHONDRIAL INTERMEMBRANE SPACE PROTEIN TRANSPORTER COMPLEX | 6 | 0.0019972 | -0.7285348 | 0.0394434 |
| 7718 | GOCC TRANSLOCON COMPLEX | 6 | 0.0020089 | -0.7281256 | 0.0395914 |
| 7419 | GOCC NUCLEOLAR EXOSOME RNASE COMPLEX | 10 | 0.0000776 | -0.7215699 | 0.0029799 |
| 9320 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0009613 | -0.7205347 | 0.0234244 |
| 4531 | GOBP PROTEIN MATURATION BY IRON SULFUR CLUSTER TRANSFER | 17 | 0.0000004 | -0.7105600 | 0.0000271 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_eos_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
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## 24/36
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## 26/36
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## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb28c6d7b6.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_eos_b_adj
myname <- "crp_eos_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 8491 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0003556 | -0.9220515 | 0.0064403 |
| 7048 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 53 | 0.0000000 | -0.8656393 | 0.0000000 |
| 8371 | GOMF HISTONE H3K4ME H3K4ME2 H3K4ME3 DEMETHYLASE ACTIVITY | 5 | 0.0009198 | 0.8557061 | 0.0134398 |
| 7537 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000063 | -0.8248306 | 0.0002017 |
| 7550 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0015200 | -0.8187506 | 0.0193219 |
| 7535 | GOCC PROTEASOME CORE COMPLEX | 18 | 0.0000000 | -0.7955861 | 0.0000003 |
| 146 | GOBP AMP SALVAGE | 5 | 0.0022326 | -0.7894699 | 0.0255105 |
| 7751 | GOCC UNIPLEX COMPLEX | 6 | 0.0009794 | -0.7770200 | 0.0140825 |
| 7125 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | 7 | 0.0003755 | -0.7761913 | 0.0066977 |
| 9186 | GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | 158 | 0.0000000 | -0.7702944 | 0.0000000 |
| 7536 | GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | 7 | 0.0004766 | -0.7624201 | 0.0080849 |
| 6253 | GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | 6 | 0.0012199 | -0.7623638 | 0.0164182 |
| 9326 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0000754 | -0.7619019 | 0.0017718 |
| 1796 | GOBP INTERNEURON MIGRATION | 5 | 0.0031722 | 0.7618805 | 0.0328097 |
| 7123 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 2B COMPLEX | 5 | 0.0032034 | -0.7610985 | 0.0329224 |
| 7695 | GOCC THO COMPLEX | 6 | 0.0012700 | -0.7596508 | 0.0169508 |
| 7275 | GOCC LSM1 7 PAT1 COMPLEX | 5 | 0.0032675 | -0.7595162 | 0.0333460 |
| 7478 | GOCC PICLN SM PROTEIN COMPLEX | 6 | 0.0013273 | -0.7566650 | 0.0174755 |
| 3284 | GOBP OBSERVATIONAL LEARNING | 6 | 0.0013488 | 0.7555737 | 0.0176574 |
| 7462 | GOCC PHAGOCYTIC VESICLE LUMEN | 5 | 0.0035437 | 0.7530054 | 0.0353650 |
| 9239 | GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | 7 | 0.0006146 | -0.7474796 | 0.0097883 |
| 7581 | GOCC RIBOSOMAL SUBUNIT | 182 | 0.0000000 | -0.7460887 | 0.0000000 |
| 7264 | GOCC LARGE RIBOSOMAL SUBUNIT | 110 | 0.0000000 | -0.7448897 | 0.0000000 |
| 8287 | GOMF GLUTAMATE GATED CALCIUM ION CHANNEL ACTIVITY | 5 | 0.0039889 | 0.7434209 | 0.0385061 |
| 7052 | GOCC CYTOSOLIC SMALL RIBOSOMAL SUBUNIT | 43 | 0.0000000 | -0.7410932 | 0.0000000 |
| 6879 | GOCC BASAL CORTEX | 5 | 0.0041606 | 0.7399836 | 0.0398676 |
| 1734 | GOBP INNER CELL MASS CELL DIFFERENTIATION | 6 | 0.0017000 | 0.7397354 | 0.0208470 |
| 3613 | GOBP POSITIVE REGULATION OF BASEMENT MEMBRANE ASSEMBLY INVOLVED IN EMBRYONIC BODY MORPHOGENESIS | 5 | 0.0041894 | 0.7394198 | 0.0400208 |
| 7638 | GOCC SMALL RIBOSOMAL SUBUNIT | 75 | 0.0000000 | -0.7362367 | 0.0000000 |
| 7133 | GOCC EXTERNAL SIDE OF APICAL PLASMA MEMBRANE | 5 | 0.0044429 | 0.7346003 | 0.0417491 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_eos_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb386626d6.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_pod1_a_adj
myname <- "crp_pod1_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 4897 | GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | 5 | 0.0003722 | 0.9189759 | 0.0053493 |
| 1263 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0000815 | 0.8597921 | 0.0015713 |
| 1796 | GOBP INTRACELLULAR GLUTAMATE HOMEOSTASIS | 5 | 0.0009510 | -0.8532944 | 0.0111001 |
| 2664 | GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 6 | 0.0005019 | 0.8202256 | 0.0066908 |
| 181 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0015606 | -0.8167733 | 0.0164027 |
| 8428 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0015606 | -0.8167733 | 0.0164027 |
| 7220 | GOCC MESSENGER RIBONUCLEOPROTEIN COMPLEX | 6 | 0.0006064 | 0.8082082 | 0.0077821 |
| 5674 | GOBP REGULATION OF TERMINATION OF DNA TEMPLATED TRANSCRIPTION | 5 | 0.0024120 | 0.7834714 | 0.0224326 |
| 7092 | GOCC F ACTIN CAPPING PROTEIN COMPLEX | 7 | 0.0003851 | 0.7747475 | 0.0054713 |
| 4970 | GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 6 | 0.0012382 | 0.7613624 | 0.0137442 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0002419 | 0.7493410 | 0.0037522 |
| 9075 | GOMF SPHINGOSINE 1 PHOSPHATE RECEPTOR ACTIVITY | 7 | 0.0005969 | -0.7492099 | 0.0077025 |
| 7759 | GOMF ADENINE TRANSMEMBRANE TRANSPORTER ACTIVITY | 5 | 0.0043344 | -0.7366340 | 0.0343901 |
| 7149 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 7 | 0.0007919 | -0.7323194 | 0.0096305 |
| 1115 | GOBP EMBRYONIC DIGESTIVE TRACT MORPHOGENESIS | 6 | 0.0019422 | 0.7304874 | 0.0194006 |
| 1748 | GOBP INTERKINETIC NUCLEAR MIGRATION | 5 | 0.0046922 | 0.7301017 | 0.0361187 |
| 1791 | GOBP INTRACELLULAR AMINO ACID HOMEOSTASIS | 7 | 0.0008825 | -0.7257568 | 0.0104533 |
| 174 | GOBP ANTEROGRADE DENDRITIC TRANSPORT | 8 | 0.0003965 | 0.7231584 | 0.0055990 |
| 8284 | GOMF HISTONE H2A UBIQUITIN LIGASE ACTIVITY | 6 | 0.0022652 | 0.7196781 | 0.0215415 |
| 2092 | GOBP MAST CELL CYTOKINE PRODUCTION | 6 | 0.0022773 | 0.7193015 | 0.0216122 |
| 7533 | GOCC SARCOPLASMIC RETICULUM LUMEN | 5 | 0.0059225 | 0.7106363 | 0.0429554 |
| 7261 | GOCC MITOTIC COHESIN COMPLEX | 7 | 0.0011757 | 0.7081266 | 0.0131921 |
| 6952 | GOCC CRD MEDIATED MRNA STABILITY COMPLEX | 5 | 0.0066451 | 0.7008471 | 0.0465257 |
| 762 | GOBP CHOLINE TRANSPORT | 5 | 0.0067883 | 0.6990211 | 0.0472793 |
| 2465 | GOBP NEGATIVE REGULATION OF ADENYLATE CYCLASE ACTIVATING ADRENERGIC RECEPTOR SIGNALING PATHWAY | 5 | 0.0068542 | 0.6981928 | 0.0474536 |
| 7414 | GOCC PLATELET DENSE GRANULE MEMBRANE | 6 | 0.0031612 | 0.6957688 | 0.0271200 |
| 6784 | GOCC ARP2 3 PROTEIN COMPLEX | 9 | 0.0003093 | 0.6943241 | 0.0046200 |
| 3539 | GOBP POSITIVE REGULATION OF AGGREPHAGY | 5 | 0.0072254 | 0.6936559 | 0.0492166 |
| 353 | GOBP BRANCHING INVOLVED IN LABYRINTHINE LAYER MORPHOGENESIS | 10 | 0.0001479 | 0.6928682 | 0.0025452 |
| 65 | GOBP ADENINE TRANSPORT | 6 | 0.0039452 | -0.6794842 | 0.0320360 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_pod1_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb50b63133.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- crp_pod1_b_adj
myname <- "crp_pod1_b_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 8265 | GOMF HEMOGLOBIN BINDING | 7 | 0.0000276 | 0.9147940 | 0.0011168 |
| 3151 | GOBP NITRIC OXIDE TRANSPORT | 5 | 0.0006876 | 0.8764872 | 0.0129785 |
| 181 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0007754 | -0.8679593 | 0.0141072 |
| 8428 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0007754 | -0.8679593 | 0.0141072 |
| 7139 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0000025 | 0.8589747 | 0.0001555 |
| 7136 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0000086 | 0.8563568 | 0.0004252 |
| 8261 | GOMF HAPTOGLOBIN BINDING | 8 | 0.0000303 | 0.8515062 | 0.0012090 |
| 4100 | GOBP POSITIVE REGULATION OF PROTEIN LOCALIZATION TO SYNAPSE | 5 | 0.0010413 | 0.8467056 | 0.0172155 |
| 7213 | GOCC MCRD MEDIATED MRNA STABILITY COMPLEX | 5 | 0.0012293 | -0.8345444 | 0.0194898 |
| 9245 | GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 5 | 0.0013539 | -0.8273908 | 0.0210009 |
| 7386 | GOCC PHAGOCYTIC VESICLE LUMEN | 5 | 0.0017360 | 0.8087349 | 0.0249298 |
| 6773 | GOCC ANKYRIN 1 COMPLEX | 5 | 0.0020571 | 0.7957831 | 0.0281160 |
| 416 | GOBP CARBOHYDRATE IMPORT ACROSS PLASMA MEMBRANE | 5 | 0.0024214 | 0.7831702 | 0.0312024 |
| 422 | GOBP CARBON DIOXIDE TRANSPORT | 8 | 0.0001467 | 0.7750412 | 0.0040804 |
| 6795 | GOCC ATP BINDING CASSETTE ABC TRANSPORTER COMPLEX | 5 | 0.0034268 | 0.7557041 | 0.0390177 |
| 2016 | GOBP L LEUCINE CATABOLIC PROCESS | 5 | 0.0039436 | -0.7443524 | 0.0435673 |
| 4896 | GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 8 | 0.0003324 | 0.7325959 | 0.0075699 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0003338 | 0.7323723 | 0.0075832 |
| 7111 | GOCC GLYCOPROTEIN IB IX V COMPLEX | 5 | 0.0046348 | 0.7311182 | 0.0486577 |
| 6832 | GOCC BRCA1 C COMPLEX | 6 | 0.0020657 | -0.7261731 | 0.0281270 |
| 4074 | GOBP POSITIVE REGULATION OF PROTEIN CATABOLIC PROCESS IN THE VACUOLE | 6 | 0.0028467 | 0.7033620 | 0.0346145 |
| 1841 | GOBP ISG15 PROTEIN CONJUGATION | 6 | 0.0029352 | -0.7011500 | 0.0352286 |
| 2710 | GOBP NEGATIVE REGULATION OF INFLAMMATORY RESPONSE TO WOUNDING | 7 | 0.0017246 | 0.6839607 | 0.0248042 |
| 3334 | GOBP OXYGEN TRANSPORT | 10 | 0.0001883 | 0.6818717 | 0.0049409 |
| 1403 | GOBP FORMATION OF TRANSLATION PREINITIATION COMPLEX | 7 | 0.0021196 | -0.6706472 | 0.0284991 |
| 6733 | GOBP WYBUTOSINE METABOLIC PROCESS | 6 | 0.0044732 | -0.6701024 | 0.0477184 |
| 8721 | GOMF OXYGEN CARRIER ACTIVITY | 9 | 0.0005134 | 0.6685914 | 0.0103722 |
| 5120 | GOBP REGULATION OF INFLAMMATORY RESPONSE TO WOUNDING | 9 | 0.0005361 | 0.6663529 | 0.0106893 |
| 1098 | GOBP ECTODERMAL CELL DIFFERENTIATION | 6 | 0.0048132 | 0.6645801 | 0.0497776 |
| 3519 | GOBP POLY N ACETYLLACTOSAMINE METABOLIC PROCESS | 7 | 0.0025427 | 0.6587055 | 0.0322732 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/RtmpDuNPu1/crp_pod1_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb61d30b67.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crplo_t0_adj
myname <- "avb_crplo_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1954 | GOBP LIPOXYGENASE PATHWAY | 9 | 0.0000044 | -0.8836792 | 0.0002816 |
| 1953 | GOBP LIPOXIN METABOLIC PROCESS | 5 | 0.0006376 | -0.8818020 | 0.0160684 |
| 8034 | GOMF COMPLEMENT COMPONENT C3B BINDING | 5 | 0.0013422 | -0.8280357 | 0.0284685 |
| 8385 | GOMF ICOSANOID BINDING | 7 | 0.0002328 | -0.8032031 | 0.0075561 |
| 182 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0024861 | -0.7811114 | 0.0441034 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0024861 | -0.7811114 | 0.0441034 |
| 4168 | GOBP POSITIVE REGULATION OF RIG I SIGNALING PATHWAY | 8 | 0.0001394 | 0.7776050 | 0.0050522 |
| 8142 | GOMF DNA RNA HYBRID BINDING | 5 | 0.0027198 | 0.7740681 | 0.0468282 |
| 1270 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0003905 | 0.7739560 | 0.0111276 |
| 9176 | GOMF SUPEROXIDE GENERATING NADPH OXIDASE ACTIVATOR ACTIVITY | 10 | 0.0000227 | -0.7734858 | 0.0011613 |
| 9304 | GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 5 | 0.0027760 | 0.7724583 | 0.0476199 |
| 7855 | GOMF ANKYRIN REPEAT BINDING | 6 | 0.0011078 | 0.7688285 | 0.0244696 |
| 5581 | GOBP REGULATION OF RESPIRATORY BURST INVOLVED IN INFLAMMATORY RESPONSE | 6 | 0.0012492 | -0.7607635 | 0.0269813 |
| 8653 | GOMF NERVE GROWTH FACTOR BINDING | 6 | 0.0017332 | -0.7383980 | 0.0344953 |
| 6410 | GOBP SYNAPSE PRUNING | 9 | 0.0001340 | -0.7350431 | 0.0049313 |
| 4533 | GOBP PROTEIN REPAIR | 7 | 0.0008970 | -0.7247666 | 0.0211861 |
| 1725 | GOBP INNATE IMMUNE RESPONSE IN MUCOSA | 17 | 0.0000003 | -0.7186010 | 0.0000261 |
| 8868 | GOMF PHOSPHOLIPASE INHIBITOR ACTIVITY | 7 | 0.0010159 | -0.7171477 | 0.0232225 |
| 8565 | GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 7 | 0.0011900 | 0.7073725 | 0.0261151 |
| 1629 | GOBP HEPOXILIN METABOLIC PROCESS | 7 | 0.0012214 | -0.7057521 | 0.0266032 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0013196 | -0.7009167 | 0.0281021 |
| 7744 | GOMF 1 PHOSPHATIDYLINOSITOL 4 PHOSPHATE 3 KINASE ACTIVITY | 7 | 0.0013429 | 0.6998190 | 0.0284685 |
| 5892 | GOBP RESPONSE TO CORTICOSTERONE | 11 | 0.0000650 | -0.6953533 | 0.0026876 |
| 8751 | GOMF OXIDOREDUCTASE ACTIVITY ACTING ON DIPHENOLS AND RELATED SUBSTANCES AS DONORS | 9 | 0.0003285 | -0.6913123 | 0.0098475 |
| 5848 | GOBP RESPIRATORY BURST INVOLVED IN INFLAMMATORY RESPONSE | 8 | 0.0011062 | -0.6659386 | 0.0244696 |
| 1771 | GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 7 | 0.0025270 | 0.6591110 | 0.0445760 |
| 5945 | GOBP RESPONSE TO INTERFERON ALPHA | 18 | 0.0000016 | 0.6532227 | 0.0001128 |
| 2622 | GOBP NEGATIVE REGULATION OF DIGESTIVE SYSTEM PROCESS | 10 | 0.0004748 | 0.6381153 | 0.0129411 |
| 7333 | GOCC NADPH OXIDASE COMPLEX | 14 | 0.0000420 | -0.6321899 | 0.0019052 |
| 8664 | GOMF NEUROTROPHIN BINDING | 8 | 0.0021731 | -0.6258233 | 0.0399935 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crplo_t0_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb63986484.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crphi_t0_adj
myname <- "avb_crphi_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 7183 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 8 | 0.0000273 | 0.8562689 | 0.0004061 |
| 2070 | GOBP MAINTENANCE OF PROTEIN LOCATION IN MITOCHONDRION | 5 | 0.0012080 | 0.8358290 | 0.0099454 |
| 8204 | GOMF FATTY ACYL COA SYNTHASE ACTIVITY | 5 | 0.0012240 | -0.8348594 | 0.0100555 |
| 7170 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0000145 | 0.8346523 | 0.0002334 |
| 8306 | GOMF HAPTOGLOBIN BINDING | 8 | 0.0000457 | 0.8321745 | 0.0006255 |
| 3494 | GOBP PLANAR CELL POLARITY PATHWAY INVOLVED IN NEURAL TUBE CLOSURE | 6 | 0.0004275 | 0.8302994 | 0.0042386 |
| 7173 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0000062 | 0.8249405 | 0.0001100 |
| 7186 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 11 | 0.0000027 | 0.8167761 | 0.0000524 |
| 8228 | GOMF GABA A RECEPTOR ACTIVITY | 5 | 0.0019113 | -0.8014178 | 0.0144215 |
| 8310 | GOMF HEMOGLOBIN BINDING | 7 | 0.0002777 | 0.7933234 | 0.0029077 |
| 7665 | GOCC TORC1 COMPLEX | 6 | 0.0013655 | 0.7547414 | 0.0109673 |
| 8406 | GOMF INOSITOL POLYPHOSPHATE 5 PHOSPHATASE ACTIVITY | 6 | 0.0013996 | 0.7530644 | 0.0111741 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0005705 | 0.7518835 | 0.0053576 |
| 6926 | GOCC CHROMOSOME PASSENGER COMPLEX | 6 | 0.0014831 | 0.7491157 | 0.0117363 |
| 2912 | GOBP NEGATIVE REGULATION OF PROTEIN LOCALIZATION TO CHROMATIN | 6 | 0.0014870 | 0.7489328 | 0.0117517 |
| 6332 | GOBP SPINDLE ELONGATION | 13 | 0.0000033 | 0.7448661 | 0.0000626 |
| 7189 | GOCC IMMUNOGLOBULIN COMPLEX | 112 | 0.0000000 | 0.7438167 | 0.0000000 |
| 8429 | GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | 6 | 0.0016470 | 0.7419197 | 0.0127572 |
| 2306 | GOBP MITOTIC SPINDLE ELONGATION | 11 | 0.0000208 | 0.7409763 | 0.0003214 |
| 6334 | GOBP SPINDLE MIDZONE ASSEMBLY | 13 | 0.0000042 | 0.7366941 | 0.0000772 |
| 9318 | GOMF UNMETHYLATED CPG BINDING | 10 | 0.0000648 | 0.7293687 | 0.0008418 |
| 1989 | GOBP LYMPHOCYTE AGGREGATION | 5 | 0.0054598 | 0.7174846 | 0.0335372 |
| 7162 | GOCC GROWTH CONE MEMBRANE | 6 | 0.0026350 | 0.7089127 | 0.0188873 |
| 1851 | GOBP ISOLEUCINE TRANSPORT | 5 | 0.0062475 | 0.7061056 | 0.0372500 |
| 7185 | GOCC IGE IMMUNOGLOBULIN COMPLEX | 5 | 0.0067200 | 0.6998857 | 0.0392170 |
| 1274 | GOBP ESTABLISHMENT OF PLANAR POLARITY INVOLVED IN NEURAL TUBE CLOSURE | 7 | 0.0014549 | 0.6947746 | 0.0115563 |
| 6956 | GOCC CMG COMPLEX | 11 | 0.0000710 | 0.6916602 | 0.0009086 |
| 2787 | GOBP NEGATIVE REGULATION OF MEIOTIC CELL CYCLE PHASE TRANSITION | 5 | 0.0074813 | 0.6906472 | 0.0422358 |
| 4978 | GOBP REGULATION OF DNA TEMPLATED DNA REPLICATION INITIATION | 14 | 0.0000083 | 0.6877484 | 0.0001426 |
| 4517 | GOBP PROTEIN O LINKED FUCOSYLATION | 5 | 0.0080382 | 0.6844089 | 0.0443940 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crphi_t0_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb337dfc9a.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crplo_eos_adj
myname <- "avb_crplo_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 8453 | GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | 5 | 0.0001528 | -0.9776848 | 0.0075826 |
| 6760 | GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | 5 | 0.0004655 | 0.9036828 | 0.0173302 |
| 8686 | GOMF NERVE GROWTH FACTOR BINDING | 6 | 0.0001787 | -0.8832810 | 0.0085113 |
| 411 | GOBP CANNABINOID SIGNALING PATHWAY | 7 | 0.0000655 | -0.8711999 | 0.0039846 |
| 183 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0007608 | -0.8693098 | 0.0246917 |
| 8512 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0007608 | -0.8693098 | 0.0246917 |
| 5275 | GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | 5 | 0.0011820 | -0.8374284 | 0.0333995 |
| 6996 | GOCC COLLAGEN TYPE IV TRIMER | 5 | 0.0014131 | -0.8242066 | 0.0380925 |
| 7386 | GOCC NLRP1 INFLAMMASOME COMPLEX | 5 | 0.0017216 | 0.8093662 | 0.0438869 |
| 8123 | GOMF C PALMITOYLTRANSFERASE ACTIVITY | 5 | 0.0017902 | -0.8064017 | 0.0452182 |
| 8696 | GOMF NEUROTROPHIN BINDING | 9 | 0.0000385 | -0.7922187 | 0.0026001 |
| 4866 | GOBP REGULATION OF CELLULAR PH REDUCTION | 6 | 0.0008598 | -0.7855984 | 0.0266059 |
| 6883 | GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 6 | 0.0008622 | -0.7854166 | 0.0266059 |
| 821 | GOBP COLLAGEN ACTIVATED TYROSINE KINASE RECEPTOR SIGNALING PATHWAY | 10 | 0.0000212 | -0.7764337 | 0.0016675 |
| 6308 | GOBP SNORNA LOCALIZATION | 6 | 0.0011348 | 0.7672138 | 0.0326210 |
| 7219 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 9 | 0.0000859 | -0.7558789 | 0.0048836 |
| 1859 | GOBP ISOLEUCINE METABOLIC PROCESS | 7 | 0.0007077 | 0.7390739 | 0.0237960 |
| 100 | GOBP ALKANESULFONATE TRANSMEMBRANE TRANSPORT | 6 | 0.0019257 | -0.7310811 | 0.0476352 |
| 7964 | GOMF C3HC4 TYPE RING FINGER DOMAIN BINDING | 6 | 0.0019320 | 0.7308538 | 0.0476352 |
| 190 | GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | 7 | 0.0010837 | -0.7131684 | 0.0316709 |
| 820 | GOBP COLLAGEN ACTIVATED SIGNALING PATHWAY | 14 | 0.0000053 | -0.7022840 | 0.0005512 |
| 7247 | GOCC INTRACILIARY TRANSPORT PARTICLE A | 8 | 0.0006005 | 0.7005025 | 0.0215012 |
| 1340 | GOBP FACIAL NERVE MORPHOGENESIS | 7 | 0.0019599 | 0.6757262 | 0.0481316 |
| 7048 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 53 | 0.0000000 | 0.6563245 | 0.0000000 |
| 6829 | GOCC ALPHA BETA T CELL RECEPTOR COMPLEX | 10 | 0.0003784 | 0.6490882 | 0.0151055 |
| 7298 | GOCC MHC CLASS II PROTEIN COMPLEX | 15 | 0.0000149 | 0.6457120 | 0.0012672 |
| 8559 | GOMF MANGANESE ION TRANSMEMBRANE TRANSPORTER ACTIVITY | 8 | 0.0015728 | -0.6452981 | 0.0410984 |
| 3799 | GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | 10 | 0.0004246 | 0.6435400 | 0.0163240 |
| 7224 | GOCC IGM IMMUNOGLOBULIN COMPLEX | 9 | 0.0008861 | -0.6398666 | 0.0271229 |
| 8596 | GOMF MHC CLASS II RECEPTOR ACTIVITY | 9 | 0.0008876 | 0.6397757 | 0.0271229 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crplo_eos_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
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## 24/36
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## 26/36
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## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb6f2bbd1.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crphi_eos_adj
myname <- "avb_crphi_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 253 | GOBP ATRIAL CARDIAC MUSCLE TISSUE DEVELOPMENT | 6 | 0.0003104 | 0.8500887 | 0.0477364 |
| 7223 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 11 | 0.0000508 | 0.7054426 | 0.0148887 |
| 2319 | GOBP MITOTIC SPINDLE ELONGATION | 11 | 0.0000668 | 0.6941886 | 0.0183410 |
| 6362 | GOBP SPINDLE ELONGATION | 13 | 0.0000409 | 0.6570125 | 0.0123745 |
| 91 | GOBP ALANINE TRANSPORT | 13 | 0.0001156 | -0.6174349 | 0.0227155 |
| 3438 | GOBP PERK MEDIATED UNFOLDED PROTEIN RESPONSE | 19 | 0.0001295 | -0.5071165 | 0.0242964 |
| 7246 | GOCC INTRACILIARY TRANSPORT PARTICLE | 22 | 0.0001045 | 0.4777764 | 0.0213045 |
| 7735 | GOCC T CELL RECEPTOR COMPLEX | 121 | 0.0000000 | 0.4520221 | 0.0000000 |
| 7226 | GOCC IMMUNOGLOBULIN COMPLEX | 109 | 0.0000000 | 0.4229731 | 0.0000000 |
| 8751 | GOMF OLFACTORY RECEPTOR ACTIVITY | 54 | 0.0000016 | -0.3777018 | 0.0009803 |
| 1068 | GOBP DNA REPLICATION INITIATION | 35 | 0.0002648 | 0.3562141 | 0.0423495 |
| 1834 | GOBP INTRACILIARY TRANSPORT | 43 | 0.0000673 | 0.3512056 | 0.0183410 |
| 295 | GOBP BASE EXCISION REPAIR | 43 | 0.0000995 | 0.3429608 | 0.0207324 |
| 7893 | GOMF ANTIGEN BINDING | 151 | 0.0000000 | 0.3426692 | 0.0000000 |
| 6227 | GOBP SENSORY PERCEPTION OF SMELL | 71 | 0.0000031 | -0.3200641 | 0.0018136 |
| 107 | GOBP ALTERNATIVE MRNA SPLICING VIA SPLICEOSOME | 67 | 0.0000128 | -0.3082554 | 0.0059215 |
| 5357 | GOBP REGULATION OF MRNA SPLICING VIA SPLICEOSOME | 98 | 0.0000139 | -0.2539694 | 0.0059215 |
| 5914 | GOBP RESPONSE TO CHEMOKINE | 67 | 0.0003315 | -0.2535381 | 0.0485881 |
| 7571 | GOCC REPLICATION FORK | 74 | 0.0002659 | 0.2451194 | 0.0423495 |
| 6942 | GOCC CENTRIOLE | 152 | 0.0000009 | 0.2307465 | 0.0006059 |
| 6223 | GOBP SENSORY PERCEPTION OF CHEMICAL STIMULUS | 103 | 0.0000873 | -0.2236885 | 0.0204816 |
| 7484 | GOCC PLASMA MEMBRANE SIGNALING RECEPTOR COMPLEX | 248 | 0.0000000 | 0.2216910 | 0.0000015 |
| 625 | GOBP CELLULAR RESPONSE TO TOPOLOGICALLY INCORRECT PROTEIN | 97 | 0.0001901 | -0.2192277 | 0.0336413 |
| 983 | GOBP DETECTION OF STIMULUS INVOLVED IN SENSORY PERCEPTION | 124 | 0.0000265 | -0.2184516 | 0.0088618 |
| 5332 | GOBP REGULATION OF MITOTIC NUCLEAR DIVISION | 107 | 0.0001740 | 0.2100208 | 0.0313893 |
| 8956 | GOMF PROTEASE BINDING | 116 | 0.0000981 | -0.2093359 | 0.0207324 |
| 5356 | GOBP REGULATION OF MRNA PROCESSING | 120 | 0.0000911 | -0.2067820 | 0.0207324 |
| 4699 | GOBP RECEPTOR INTERNALIZATION | 104 | 0.0003255 | -0.2039401 | 0.0484708 |
| 1075 | GOBP DNA TEMPLATED DNA REPLICATION | 160 | 0.0000152 | 0.1981209 | 0.0059493 |
| 6074 | GOBP RESPONSE TO TOPOLOGICALLY INCORRECT PROTEIN | 140 | 0.0000960 | -0.1909047 | 0.0207324 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crphi_eos_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbbf9dd1dd.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crplo_pod1_adj
myname <- "avb_crplo_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 4970 | GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 6 | 0.0002538 | 0.8623178 | 0.0284566 |
| 1263 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0001084 | 0.8447708 | 0.0162399 |
| 1764 | GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 7 | 0.0002646 | 0.7960490 | 0.0289210 |
| 4393 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0000525 | 0.7041282 | 0.0088614 |
| 8588 | GOMF NADPLUS NUCLEOTIDASE CYCLIC ADP RIBOSE GENERATING | 13 | 0.0001490 | 0.6074388 | 0.0203597 |
| 4007 | GOBP POSITIVE REGULATION OF NITRIC OXIDE SYNTHASE BIOSYNTHETIC PROCESS | 14 | 0.0001472 | 0.5858226 | 0.0203597 |
| 5916 | GOBP RESPONSE TO INTERFERON ALPHA | 18 | 0.0000733 | 0.5397536 | 0.0119544 |
| 4107 | GOBP POSITIVE REGULATION OF PROTEIN POLYUBIQUITINATION | 16 | 0.0002004 | 0.5368637 | 0.0245013 |
| 2292 | GOBP MITOTIC SISTER CHROMATID COHESION | 31 | 0.0000025 | 0.4883520 | 0.0011122 |
| 1041 | GOBP DNA DOUBLE STRAND BREAK PROCESSING | 20 | 0.0002479 | 0.4732445 | 0.0284401 |
| 7259 | GOCC MITOCHONDRIA ASSOCIATED ENDOPLASMIC RETICULUM MEMBRANE CONTACT SITE | 20 | 0.0003804 | 0.4589083 | 0.0384143 |
| 5516 | GOBP REGULATION OF PROTEIN POLYUBIQUITINATION | 24 | 0.0005177 | 0.4093104 | 0.0467553 |
| 8196 | GOMF GDP BINDING | 64 | 0.0000004 | 0.3668236 | 0.0004618 |
| 1272 | GOBP ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 42 | 0.0000608 | 0.3575099 | 0.0100912 |
| 3050 | GOBP NEGATIVE REGULATION OF VIRAL GENOME REPLICATION | 50 | 0.0000818 | 0.3219658 | 0.0126646 |
| 257 | GOBP ATTACHMENT OF SPINDLE MICROTUBULES TO KINETOCHORE | 51 | 0.0001342 | 0.3090607 | 0.0191753 |
| 8108 | GOMF DOUBLE STRANDED RNA BINDING | 70 | 0.0000090 | 0.3068283 | 0.0030604 |
| 5764 | GOBP REGULATION OF VIRAL GENOME REPLICATION | 78 | 0.0000100 | 0.2892247 | 0.0032076 |
| 816 | GOBP COLLAGEN METABOLIC PROCESS | 73 | 0.0002298 | -0.2493319 | 0.0270237 |
| 4452 | GOBP PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 71 | 0.0004858 | 0.2394074 | 0.0448067 |
| 4383 | GOBP PROTEIN DEUBIQUITINATION | 82 | 0.0004196 | 0.2253151 | 0.0401945 |
| 4485 | GOBP PROTEIN MODIFICATION BY SMALL PROTEIN REMOVAL | 102 | 0.0000862 | 0.2249743 | 0.0131296 |
| 1164 | GOBP ENDOPLASMIC RETICULUM TO GOLGI VESICLE MEDIATED TRANSPORT | 132 | 0.0000084 | 0.2245417 | 0.0029950 |
| 7558 | GOCC SITE OF DOUBLE STRAND BREAK | 94 | 0.0002357 | 0.2194419 | 0.0273791 |
| 6698 | GOBP VIRAL GENOME REPLICATION | 117 | 0.0000808 | 0.2109634 | 0.0126646 |
| 6890 | GOCC CHROMOSOME CENTROMERIC REGION | 242 | 0.0000000 | 0.2093685 | 0.0000624 |
| 4420 | GOBP PROTEIN K48 LINKED UBIQUITINATION | 97 | 0.0004099 | 0.2076017 | 0.0400863 |
| 5765 | GOBP REGULATION OF VIRAL PROCESS | 143 | 0.0000266 | 0.2034902 | 0.0053632 |
| 9243 | GOMF UBIQUITIN LIKE PROTEIN PEPTIDASE ACTIVITY | 106 | 0.0003359 | 0.2015710 | 0.0346802 |
| 7557 | GOCC SITE OF DNA DAMAGE | 125 | 0.0001676 | 0.1948981 | 0.0218370 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crplo_pod1_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]
## 11/36
## 12/36 [input_geneset_metrics1]
## 13/36
## 14/36 [input_geneset_metrics2]## 15/36
## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]
## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb7c929d01.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEde <- avb_crphi_pod1_adj
myname <- "avb_crphi_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$enrichment_result,p.adjustANOVA<0.05),30)
mtop |> kbl(caption=paste(myname,"GO")) |> kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 7149 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 7 | 0.0000061 | 0.9867404 | 0.0009990 |
| 7150 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 10 | 0.0000001 | 0.9748341 | 0.0000298 |
| 8860 | GOMF PRIMARY AMINE OXIDASE ACTIVITY | 7 | 0.0000689 | -0.8685332 | 0.0066705 |
| 8265 | GOMF HEMOGLOBIN BINDING | 7 | 0.0000919 | 0.8535119 | 0.0081419 |
| 2439 | GOBP NAIL DEVELOPMENT | 5 | 0.0010481 | 0.8462349 | 0.0468163 |
| 7151 | GOCC IGM IMMUNOGLOBULIN COMPLEX | 8 | 0.0000660 | 0.8145564 | 0.0064550 |
| 6764 | GOCC ALPHA BETA T CELL RECEPTOR COMPLEX | 10 | 0.0000086 | 0.8125029 | 0.0013523 |
| 7153 | GOCC IMMUNOGLOBULIN COMPLEX | 106 | 0.0000000 | 0.8016615 | 0.0000000 |
| 7154 | GOCC IMMUNOGLOBULIN COMPLEX CIRCULATING | 11 | 0.0000706 | 0.6919482 | 0.0067576 |
| 1468 | GOBP GLOMERULAR MESANGIAL CELL PROLIFERATION | 8 | 0.0007599 | 0.6873617 | 0.0377035 |
| 6923 | GOCC CMG COMPLEX | 11 | 0.0001053 | 0.6751633 | 0.0088799 |
| 4342 | GOBP PROLINE METABOLIC PROCESS | 8 | 0.0010159 | 0.6708520 | 0.0460410 |
| 3535 | GOBP POSITIVE REGULATION OF ACUTE INFLAMMATORY RESPONSE TO ANTIGENIC STIMULUS | 8 | 0.0011755 | 0.6624147 | 0.0489762 |
| 7136 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0007163 | 0.6511956 | 0.0361707 |
| 7139 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0006194 | 0.6250435 | 0.0326985 |
| 7004 | GOCC DNA REPLICATION PREINITIATION COMPLEX | 12 | 0.0001865 | 0.6228756 | 0.0141979 |
| 3334 | GOBP OXYGEN TRANSPORT | 10 | 0.0008134 | 0.6113920 | 0.0387562 |
| 4675 | GOBP REGULATION OF ACUTE INFLAMMATORY RESPONSE TO ANTIGENIC STIMULUS | 14 | 0.0002952 | 0.5586287 | 0.0193145 |
| 7362 | GOCC OUTER KINETOCHORE | 18 | 0.0000518 | 0.5509562 | 0.0054653 |
| 8514 | GOMF MHC CLASS I RECEPTOR ACTIVITY | 12 | 0.0011137 | 0.5434694 | 0.0479557 |
| 692 | GOBP CELL PROLIFERATION INVOLVED IN KIDNEY DEVELOPMENT | 14 | 0.0006301 | 0.5275874 | 0.0330769 |
| 8715 | GOMF OXIDOREDUCTASE ACTIVITY ACTING ON THE CH NH2 GROUP OF DONORS OXYGEN AS ACCEPTOR | 14 | 0.0007563 | -0.5198725 | 0.0377035 |
| 2281 | GOBP MITOTIC DNA REPLICATION | 17 | 0.0003534 | 0.5004266 | 0.0218882 |
| 2986 | GOBP NEGATIVE REGULATION OF SYSTEMIC ARTERIAL BLOOD PRESSURE | 16 | 0.0010979 | -0.4712883 | 0.0476644 |
| 6444 | GOBP THYMIC T CELL SELECTION | 21 | 0.0002679 | 0.4593516 | 0.0177768 |
| 2128 | GOBP MEIOTIC SPINDLE ORGANIZATION | 17 | 0.0011149 | 0.4566164 | 0.0479557 |
| 1069 | GOBP DNA UNWINDING INVOLVED IN DNA REPLICATION | 21 | 0.0003134 | 0.4542335 | 0.0202240 |
| 7659 | GOCC T CELL RECEPTOR COMPLEX | 119 | 0.0000000 | 0.4535151 | 0.0000000 |
| 7815 | GOMF ANTIGEN BINDING | 149 | 0.0000000 | 0.4460410 | 0.0000000 |
| 8345 | GOMF IMMUNOGLOBULIN RECEPTOR BINDING | 19 | 0.0011878 | 0.4295494 | 0.0492003 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/avb_crphi_pod1_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
## 3/36
## 4/36 [peek]
## 5/36
## 6/36 [metrics]
## 7/36
## 8/36 [scatterplot]## 9/36
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## 12/36 [input_geneset_metrics1]
## 13/36
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## 16/36 [input_geneset_metrics3]## 17/36
## 18/36 [echart1d]
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## 21/36 [heatmap]
## 22/36
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## 28/36
## 29/36 [detailed_geneset_reports1d]## 30/36
## 31/36 [detailed_geneset_reports2d]
## 32/36
## 33/36 [network]## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb6ebc822.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEMulti-contrast enrichment anslysis.
l2 <- list("crp_t0_a"=crp_t0_a_adj,
"crp t0 b"=crp_t0_b_adj,
"crp eos a"=crp_eos_a_adj,
"crp eos b"=crp_eos_b_adj,
"crp _pod1 a"=crp_pod1_a_adj,
"crp pod1 b"=crp_pod1_b_adj,
"avb crplo t0"=avb_crplo_t0_adj,
"avb crphi t0"=avb_crphi_t0_adj,
"avb crplo eos"=avb_crplo_eos_adj,
"avb crphi eos"=avb_crphi_eos_adj,
"avb crplo pod1"=avb_crplo_pod1_adj,
"avb crphi pod1"=avb_crphi_pod1_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm2 <- mitch_calc(x=m2,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:15)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top GOs in multi enrichment analysis") |>
kable_paper("hover", full_width = F)| crp_t0_a | crp.t0.b | crp.eos.a | crp.eos.b | crp._pod1.a | crp.pod1.b | avb.crplo.t0 | avb.crphi.t0 | avb.crplo.eos | avb.crphi.eos | avb.crplo.pod1 | avb.crphi.pod1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.9772863 | -0.1513958 | -0.8248157 | -0.7277215 | -0.8154183 | -0.8672374 | -0.7827175 | 0.3877586 | -0.8720883 | -0.3432824 | -0.5661388 | -0.5058924 |
| GOMF LIPID ANTIGEN BINDING | -0.9772863 | -0.1513958 | -0.8248157 | -0.7277215 | -0.8154183 | -0.8672374 | -0.7827175 | 0.3877586 | -0.8720883 | -0.3432824 | -0.5661388 | -0.5058924 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.8176321 | 0.3074231 | -0.8559402 | 0.3784135 | -0.7304433 | 0.3926822 | -0.5288466 | 0.9653610 | -0.7973569 | 0.6854765 | -0.4238695 | 0.9866282 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.7040814 | 0.2422985 | -0.7386072 | 0.3795167 | -0.5459423 | 0.4052707 | -0.0887261 | 0.8876415 | -0.6149367 | 0.7413852 | -0.2218914 | 0.9746551 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1435012 | 0.6828459 | -0.1372236 | 0.7577400 | -0.1377562 | 0.8112332 | -0.7357112 | 0.6567080 | -0.5790745 | 0.1831265 | -0.8471109 | 0.5190374 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.2630047 | -0.4091026 | 0.2474057 | 0.7023636 | 0.6807343 | 0.3249441 | -0.6098540 | -0.1843439 | -0.9779902 | -0.8812765 | 0.4342132 | -0.3078613 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.2565721 | -0.8110005 | 0.5939392 | 0.4722881 | 0.8614031 | -0.4579242 | 0.7744046 | -0.0155665 | -0.1149720 | -0.0780771 | 0.8442263 | -0.0885680 |
| GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 0.4691207 | -0.9036667 | 0.4065345 | 0.1409711 | 0.2105008 | -0.8263376 | 0.7730727 | -0.4398630 | -0.0885433 | 0.4333000 | 0.7371189 | -0.1842678 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8968754 | 0.1635326 | -0.8201360 | -0.9202549 | -0.3959386 | -0.4307509 | -0.2687877 | 0.3940743 | 0.7311647 | -0.1680221 | -0.1533172 | 0.0361916 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.7476578 | 0.2309697 | -0.3077472 | 0.5061778 | 0.4883721 | 0.4842821 | -0.6555857 | 0.2947924 | -0.6791363 | -0.8289057 | -0.0245304 | 0.0283921 |
| GOMF HEMOGLOBIN BINDING | 0.1832173 | 0.4423917 | 0.0951045 | 0.4996025 | 0.4206081 | 0.9159368 | 0.0708205 | 0.7899779 | -0.2173807 | -0.0914218 | 0.3406625 | 0.8529506 |
| GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | -0.2339183 | -0.3676131 | 0.3663385 | 0.1124935 | 0.5426452 | -0.3070623 | -0.3605555 | -0.2101964 | -0.8408332 | -0.8155705 | 0.7958625 | -0.3454321 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8528749 | 0.0632425 | -0.7918866 | -0.8147525 | 0.1666144 | -0.3834784 | -0.4637561 | 0.6158463 | 0.4196224 | -0.1887002 | -0.0373330 | 0.0142388 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.1280954 | -0.8113447 | 0.4112369 | 0.2618028 | 0.7632931 | -0.3513428 | 0.4078125 | -0.3011192 | -0.3882812 | -0.3939725 | 0.8619170 | 0.2531152 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.8338033 | -0.1294853 | -0.5952438 | -0.3631255 | -0.4672601 | -0.6066452 | -0.4781043 | 0.3901682 | -0.7187158 | -0.2820656 | -0.3736164 | -0.2184950 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8170290 | 0.1512411 | -0.7174489 | -0.8739477 | -0.3355412 | -0.3955452 | -0.3507315 | 0.3809104 | 0.6510816 | 0.0098280 | -0.0298104 | 0.0221713 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7866553 | -0.5168498 | -0.7390213 | -0.2598469 | 0.5222333 | -0.2271651 | -0.1640462 | 0.5086698 | 0.0176059 | -0.5793408 | 0.5912493 | 0.2668284 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.8342789 | 0.3530287 | -0.7173977 | -0.4390488 | 0.1851877 | -0.2089281 | -0.7034958 | 0.7470902 | -0.0874809 | -0.1805674 | -0.3658434 | -0.1429251 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.7961374 | 0.3611360 | -0.5761393 | -0.8208163 | 0.0530872 | -0.1048045 | -0.5830083 | 0.4427172 | 0.5694796 | -0.1782228 | -0.2331843 | 0.3403292 |
| GOCC HEMOGLOBIN COMPLEX | 0.2762249 | 0.6562078 | 0.0857102 | 0.3017791 | 0.4349348 | 0.8603273 | -0.1475502 | 0.8220436 | -0.3171725 | -0.3182476 | 0.1156217 | 0.6242127 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | -0.4394065 | -0.2161697 | -0.4336234 | 0.3311266 | 0.7125410 | 0.2112427 | 0.4175298 | 0.6248823 | 0.1127978 | -0.4698435 | 0.8001046 | 0.5541542 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.6212394 | 0.2796292 | -0.5345744 | 0.2556920 | -0.3903023 | 0.3856676 | -0.0213855 | 0.7555694 | -0.5275896 | 0.4438053 | -0.0726530 | 0.7994634 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8241652 | 0.1979165 | -0.8519266 | -0.7085054 | 0.1364666 | -0.2207211 | -0.4831890 | 0.6029493 | 0.3694986 | -0.0879840 | -0.0660070 | -0.0188755 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.2340453 | 0.5244996 | 0.0163260 | 0.3343587 | 0.4396930 | 0.8577537 | -0.0575824 | 0.8319301 | -0.3402570 | -0.1060902 | 0.3244330 | 0.6504463 |
| GOMF UNMETHYLATED CPG BINDING | -0.2279612 | 0.5854914 | 0.0504329 | 0.6650937 | -0.1432690 | 0.6088479 | 0.5110741 | 0.7256874 | 0.3617734 | 0.4910570 | -0.4589002 | 0.3351727 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.2727258 | -0.0087035 | -0.3031326 | 0.2990742 | -0.2340911 | 0.4085101 | -0.7001807 | -0.3326516 | -0.8967786 | -0.7998668 | -0.3956371 | 0.1338343 |
| GOMF HAPTOGLOBIN BINDING | 0.3446062 | 0.6114203 | 0.0960926 | 0.2880280 | 0.3774020 | 0.8528111 | -0.0348411 | 0.8294568 | -0.2845914 | -0.1975956 | 0.2407962 | 0.6102906 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 0.2844165 | -0.3690233 | -0.0441719 | -0.3750705 | -0.2450076 | -0.6357669 | 0.6591677 | -0.3797180 | 0.4770579 | -0.3367624 | 0.7959028 | 0.5628198 |
| GOBP HYPOXIA INDUCIBLE FACTOR 1ALPHA SIGNALING PATHWAY | 0.4300471 | -0.7090788 | 0.6424026 | 0.0209540 | 0.3817473 | -0.5990869 | 0.3908023 | -0.2389785 | 0.3914491 | 0.3830409 | 0.7427878 | -0.0264517 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.7544171 | 0.1613418 | -0.7248305 | -0.7589730 | -0.4147680 | -0.3606579 | -0.2991274 | 0.4630854 | 0.5809986 | 0.0129752 | -0.0440840 | 0.0958157 |
| GOBP POSITIVE REGULATION OF PYROPTOSIS | 0.3971370 | -0.4186332 | 0.5448519 | -0.4377324 | -0.1985923 | -0.4611119 | 0.5920673 | -0.0876302 | 0.7469920 | 0.3953108 | 0.3012413 | 0.6239692 |
| GOCC CHROMOSOME PASSENGER COMPLEX | -0.5230825 | 0.0067218 | -0.6686166 | 0.1920162 | 0.0284093 | 0.5281081 | 0.1918101 | 0.7445227 | -0.2589334 | 0.7314436 | -0.0755255 | 0.6154761 |
| GOMF LIGAND GATED MONOATOMIC ION CHANNEL ACTIVITY INVOLVED IN REGULATION OF PRESYNAPTIC MEMBRANE POTENTIAL | -0.0817711 | 0.2319209 | -0.5624673 | 0.4788034 | -0.5033433 | 0.4508584 | 0.0275550 | 0.4403006 | -0.4395396 | 0.7460408 | -0.6946592 | 0.1512627 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | -0.1743948 | -0.2626052 | 0.0482713 | -0.3568079 | -0.2249203 | -0.5204451 | 0.5945784 | 0.1137490 | 0.9009654 | 0.6738289 | 0.5560375 | 0.0927094 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.2978852 | 0.1318209 | -0.0288532 | 0.3867117 | 0.4903453 | 0.5435810 | -0.7394654 | 0.0782840 | -0.8856971 | -0.5661245 | 0.0111925 | 0.1116871 |
| GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | -0.6602276 | 0.2783149 | -0.5922134 | -0.7423883 | -0.3036725 | -0.1778359 | -0.3684797 | 0.3767284 | 0.6159810 | 0.0447019 | -0.3027213 | 0.4108238 |
| GOCC BRCA1 C COMPLEX | 0.2449507 | -0.7906085 | 0.4815784 | -0.1957893 | 0.3528013 | -0.7246108 | 0.4314817 | -0.1821713 | -0.1987539 | 0.2954913 | 0.6994039 | -0.1173468 |
| GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | -0.5567861 | -0.2985765 | -0.4864617 | -0.7572821 | 0.3559232 | -0.5302735 | -0.3714557 | -0.0065568 | 0.4413317 | -0.4099405 | 0.4902531 | 0.2899202 |
| GOCC PICLN SM PROTEIN COMPLEX | -0.6348648 | 0.0355909 | -0.6159834 | -0.7520213 | 0.1518279 | -0.5089572 | -0.4312122 | 0.2478043 | 0.6597546 | -0.1296332 | 0.2616919 | -0.1436158 |
| GOMF PROTEASOME ACTIVATING ACTIVITY | -0.6326611 | 0.1256381 | -0.6714385 | -0.6502426 | 0.4853832 | -0.2196011 | -0.4205587 | 0.4140746 | 0.5200545 | -0.2677637 | 0.1958845 | 0.3426551 |
| GOCC SIGNAL PEPTIDASE COMPLEX | -0.6047748 | -0.5276359 | -0.5626385 | -0.4552337 | 0.3505873 | -0.7246397 | -0.1701907 | 0.1556570 | 0.0225710 | -0.3328197 | 0.6439245 | 0.0947829 |
| GOMF NEUROTROPHIN BINDING | -0.1987770 | 0.0564838 | 0.0410192 | 0.3139596 | 0.4994259 | 0.5770477 | -0.6830984 | 0.0214914 | -0.8887855 | -0.6044845 | -0.0274028 | 0.2028673 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.7325914 | -0.2501831 | -0.5172683 | -0.5184477 | -0.0622152 | -0.5629429 | -0.4432682 | 0.1154040 | -0.1028487 | 0.4305797 | -0.2434299 | -0.6663718 |
| GOCC IMMUNOGLOBULIN COMPLEX CIRCULATING | -0.5751521 | 0.2107373 | -0.6009445 | 0.3288530 | -0.4067923 | 0.2123374 | 0.1589450 | 0.6320217 | -0.3906959 | 0.5008714 | 0.0440123 | 0.6914947 |
| GOBP OXYGEN TRANSPORT | 0.2810865 | 0.4898202 | 0.2293312 | 0.3483113 | 0.4350966 | 0.6833413 | -0.0279326 | 0.7253449 | -0.3113405 | -0.2472553 | 0.3645229 | 0.6105509 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7505434 | 0.0600932 | -0.7635932 | -0.7016619 | 0.1550594 | -0.2980004 | -0.4259651 | 0.5276442 | 0.3164034 | -0.1004032 | -0.0765880 | -0.0762888 |
| GOCC IGM IMMUNOGLOBULIN COMPLEX | -0.3729904 | 0.3857377 | -0.3187666 | 0.2198916 | -0.4647546 | 0.5718108 | -0.1337281 | 0.4724482 | -0.6199344 | 0.1964659 | -0.1468560 | 0.8141767 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.4390831 | -0.0902934 | -0.6257383 | -0.1749275 | -0.5384981 | -0.7428259 | -0.2453512 | 0.3748038 | 0.1639321 | 0.7273410 | 0.2453512 | 0.2017882 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.7552105 | 0.1429878 | -0.8293632 | -0.6375733 | 0.0890513 | -0.2079840 | -0.4603930 | 0.5415137 | 0.2198268 | -0.0683374 | -0.1220910 | -0.0204467 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.6983348 | 0.1448553 | -0.6763233 | -0.7693276 | -0.2926736 | -0.3556972 | -0.2631109 | 0.3718961 | 0.5728972 | -0.0309452 | -0.0133323 | 0.0473107 |
mitch_report(res=mm2,outfile="multigostratified_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/RtmpDuNPu1/multigostratified_all_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/36
## 2/36 [checklibraries]
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## 6/36 [metrics]
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## 8/36 [scatterplot]## 9/36
## 10/36 [contourplot]## 11/36
## 12/36 [input_geneset_metrics1]
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## 16/36 [input_geneset_metrics3]
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## 18/36 [echart1d]
## 19/36 [echart2d]
## 20/36
## 21/36 [heatmap]## 22/36
## 23/36 [effectsize]
## 24/36
## 25/36 [results_table]
## 26/36
## 27/36 [results_table_complete]
## 28/36
## 29/36 [detailed_geneset_reports1d]
## 30/36
## 31/36 [detailed_geneset_reports2d]## 32/36
## 33/36 [network]
## 34/36
## 35/36 [session_info]
## 36/36## output file: /paddi-genomics/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /paddi-genomics/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpDuNPu1/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb16b14841.html##
## Output created: /tmp/RtmpDuNPu1/mitch_report.html## [1] TRUEThis might work better if we work on each timepoint separately.
l2 <- list("crp_t0_a"=crp_t0_a_adj, "crp t0 b"=crp_t0_b_adj,
"avb crplo t0"=avb_crplo_t0_adj, "avb crphi t0"=avb_crphi_t0_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top GOs in multi enrichment analysis stratified t0") |>
kable_paper("hover", full_width = F)| crp_t0_a | crp.t0.b | avb.crplo.t0 | avb.crphi.t0 | |
|---|---|---|---|---|
| GOBP MAINTENANCE OF PROTEIN LOCATION IN MITOCHONDRION | -0.9185182 | 0.5244089 | -0.6907935 | 0.8358290 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.8370894 | 0.3520037 | -0.7009167 | 0.7518835 |
| GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 0.4598125 | -0.9053464 | 0.7724583 | -0.4308164 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.9778642 | -0.1546124 | -0.7811114 | 0.3957283 |
| GOMF LIPID ANTIGEN BINDING | -0.9778642 | -0.1546124 | -0.7811114 | 0.3957283 |
| GOBP PLANAR CELL POLARITY PATHWAY INVOLVED IN NEURAL TUBE CLOSURE | -0.7165813 | 0.6240090 | -0.1201061 | 0.8302994 |
| GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | -0.7786773 | 0.4172308 | -0.4980485 | 0.7419197 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.6374531 | 0.3266970 | -0.5350037 | 0.8562689 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1534782 | 0.6825612 | -0.7345164 | 0.6630780 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | -0.7705174 | 0.2094423 | -0.5770171 | 0.6398047 |
| GOCC MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX III | -0.7280744 | 0.2918173 | -0.5508274 | 0.6718859 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8562451 | 0.0608187 | -0.4615870 | 0.6220261 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8278774 | 0.1960567 | -0.4816011 | 0.6093138 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.2460190 | -0.8135271 | 0.7739560 | -0.0045543 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.8007136 | 0.3600549 | -0.5803843 | 0.4508875 |
| GOMF OXIDOREDUCTASE ACTIVITY ACTING ON DIPHENOLS AND RELATED SUBSTANCES AS DONORS | -0.7169592 | 0.1677721 | -0.6913123 | 0.5117129 |
| GOBP POSITIVE REGULATION OF PLASMINOGEN ACTIVATION | -0.7151221 | 0.1834476 | -0.6074908 | 0.5721800 |
| GOBP LIPOXYGENASE PATHWAY | -0.5081856 | 0.3247945 | -0.8836792 | 0.3016585 |
| GOBP GLYCOLYTIC PROCESS THROUGH GLUCOSE 6 PHOSPHATE | -0.6973987 | 0.3673501 | -0.4750544 | 0.6086349 |
| GOCC HEMOGLOBIN COMPLEX | 0.2708417 | 0.6556999 | -0.1457914 | 0.8249405 |
| GOMF UNMETHYLATED CPG BINDING | -0.2375572 | 0.5851235 | 0.5107685 | 0.7293687 |
| GOBP NAD CATABOLIC PROCESS | -0.6328820 | 0.4397029 | -0.5008972 | 0.5887169 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7906243 | -0.5197988 | -0.1628264 | 0.5147130 |
| GOMF HAPTOGLOBIN BINDING | 0.3384526 | 0.6108316 | -0.0330940 | 0.8321745 |
| GOBP SEQUESTERING OF METAL ION | -0.7585079 | 0.2058595 | -0.4964207 | 0.5051574 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5364526 | 0.5211001 | -0.6487529 | -0.3578333 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.7598235 | 0.1411658 | -0.4587687 | 0.5474078 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.8364491 | -0.1317098 | -0.4769506 | 0.3976124 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.5855254 | 0.2615981 | -0.1337207 | 0.8167761 |
| GOMF FATTY ACYL COA SYNTHASE ACTIVITY | 0.4852047 | -0.2471072 | -0.3138440 | -0.8348594 |
| GOMF PROTON TRANSPORTING ATP SYNTHASE ACTIVITY ROTATIONAL MECHANISM | -0.7645683 | 0.0486181 | -0.4098964 | 0.5795793 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8993094 | 0.1616007 | -0.2667002 | 0.4034118 |
| GOCC RESPIRATORY CHAIN COMPLEX IV | -0.6875195 | 0.1263524 | -0.5258078 | 0.5497437 |
| GOMF ICOSANOID BINDING | -0.2709666 | 0.5221019 | -0.8032031 | 0.2430394 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7549370 | 0.0578538 | -0.4241602 | 0.5339004 |
| GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | -0.5967437 | -0.4863023 | -0.6560713 | -0.0641482 |
| GOCC CASPASE COMPLEX | -0.7129541 | 0.1703643 | -0.2078842 | 0.6678408 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.2277369 | 0.5235351 | -0.0558122 | 0.8346523 |
| GOCC CYTOCHROME COMPLEX | -0.6608643 | 0.1983565 | -0.5099558 | 0.5344277 |
| GOBP GLYCERALDEHYDE 3 PHOSPHATE METABOLIC PROCESS | -0.6921409 | 0.2034675 | -0.5488289 | 0.4400640 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.7767024 | -0.3097582 | -0.0785842 | 0.5525602 |
| GOMF SULFATIDE BINDING | -0.7163137 | -0.1718088 | 0.2147633 | 0.6486440 |
| GOMF PORIN ACTIVITY | -0.7783876 | -0.1799610 | -0.5231126 | 0.3007379 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.5987601 | 0.2980817 | -0.0190012 | 0.7438167 |
| GOBP PROTEIN REPAIR | -0.5853791 | 0.1585392 | -0.7247666 | 0.3261283 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT CYTOCHROME C TO OXYGEN | -0.6486719 | 0.1124789 | -0.5228609 | 0.5267710 |
| GOMF SUPEROXIDE GENERATING NADPH OXIDASE ACTIVATOR ACTIVITY | -0.2472827 | 0.5558097 | -0.7734858 | -0.0689936 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8206756 | 0.1491799 | -0.3483891 | 0.3898475 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.7362331 | 0.2621661 | -0.5439993 | 0.2215667 |
| GOBP MITOCHONDRIAL RESPIRASOME ASSEMBLY | -0.6757209 | -0.1295666 | -0.5147836 | 0.4564986 |
#mitch_report(res=mm2,outfile="multigostratified_t0_mitchreport.html",overwrite=TRUE)
l2 <- list("crp_eos_a"=crp_eos_a_adj, "crp eos b"=crp_eos_b_adj,
"avb crplo eos"=avb_crplo_eos_adj, "avb crphi eos"=avb_crphi_eos_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top GOs in multi enrichment analysis stratified EOS") |>
kable_paper("hover", full_width = F)| crp_eos_a | crp.eos.b | avb.crplo.eos | avb.crphi.eos | |
|---|---|---|---|---|
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | 0.2428299 | 0.6966991 | -0.9776848 | -0.8783123 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8228244 | -0.9220515 | 0.7377648 | -0.1594435 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8273165 | -0.7330908 | -0.8693098 | -0.3377467 |
| GOMF LIPID ANTIGEN BINDING | -0.8273165 | -0.7330908 | -0.8693098 | -0.3377467 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | 0.6984996 | 0.5729017 | -0.6586705 | -0.7976539 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.7053402 | -0.8656393 | 0.6563245 | 0.0215005 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.7437528 | 0.4235368 | -0.6298229 | 0.7054426 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.5771756 | -0.6573065 | 0.5938165 | 0.6981722 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.4734385 | -0.7623638 | 0.6844905 | 0.5539187 |
| GOCC COLLAGEN TYPE IV TRIMER | 0.2623443 | 0.6946622 | -0.8242066 | -0.5627353 |
| GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | -0.7827732 | -0.6238938 | 0.6435400 | -0.3289918 |
| GOCC EXTRINSIC COMPONENT OF MITOCHONDRIAL INNER MEMBRANE | -0.6701981 | -0.6577851 | 0.5828976 | 0.5476439 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.7951078 | -0.8187506 | 0.4310448 | -0.1793762 |
| GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 0.5940223 | 0.7164249 | -0.6227436 | -0.5023871 |
| GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | 0.3632263 | 0.1029190 | -0.8374284 | -0.8120760 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.3969748 | 0.3117204 | -0.7238818 | -0.8398884 |
| GOCC EXTERNAL SIDE OF APICAL PLASMA MEMBRANE | 0.2237337 | 0.7346003 | -0.6921888 | -0.6438665 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.1575378 | 0.3694460 | -0.8711999 | -0.7458946 |
| GOBP SCARNA LOCALIZATION TO CAJAL BODY | -0.7423661 | -0.6362099 | 0.6877148 | -0.1973084 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 0.3146910 | 0.7113779 | -0.7854166 | -0.4893830 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.7287151 | -0.7619019 | 0.5900965 | 0.0214340 |
| GOCC ANKYRIN 1 COMPLEX | 0.6183634 | 0.6520711 | -0.1722215 | -0.7735795 |
| GOCC IGE IMMUNOGLOBULIN COMPLEX | -0.8023461 | 0.3879058 | -0.4882422 | 0.6340820 |
| GOBP ISOLEUCINE METABOLIC PROCESS | -0.5195785 | -0.4291950 | 0.7390739 | 0.6547965 |
| GOCC PICLN SM PROTEIN COMPLEX | -0.6201216 | -0.7566650 | 0.6679550 | -0.1212962 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | 0.0434118 | -0.3662453 | 0.9036828 | 0.6773302 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8541271 | -0.7134658 | 0.3808359 | -0.0793397 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.6746353 | -0.7702944 | 0.5810197 | -0.0213325 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.5809905 | -0.8248306 | 0.5795261 | -0.1696667 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.6444040 | 0.4148856 | -0.7558789 | 0.4670709 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 2B COMPLEX | -0.5587524 | -0.7610985 | 0.6836592 | -0.0318632 |
| GOCC CHAPERONIN CONTAINING T COMPLEX | -0.6783892 | -0.6330453 | 0.6043454 | -0.3292810 |
| GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | -0.5968144 | -0.7474796 | 0.6250325 | 0.0531102 |
| GOCC LARGE RIBOSOMAL SUBUNIT | -0.6679071 | -0.7448897 | 0.5453707 | -0.0504811 |
| GOCC BOX C D RNP COMPLEX | -0.6008366 | -0.6856415 | 0.6183323 | -0.2886969 |
| GOCC MITOCHONDRIAL INTERMEMBRANE SPACE PROTEIN TRANSPORTER COMPLEX | -0.7285348 | -0.6905682 | 0.5186953 | 0.1175829 |
| GOCC RIBOSOMAL SUBUNIT | -0.6475442 | -0.7460887 | 0.5510150 | -0.0370963 |
| GOCC METHYLOSOME | -0.6929322 | -0.6554403 | 0.5876200 | -0.1489138 |
| GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | -0.7005878 | -0.7268317 | 0.5071698 | 0.0020912 |
| GOCC PROTEASOME CORE COMPLEX | -0.5381011 | -0.7955861 | 0.5128267 | -0.2751669 |
| GOMF C PALMITOYLTRANSFERASE ACTIVITY | 0.2282259 | 0.0595435 | -0.8064017 | -0.7395108 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.0327225 | 0.3816517 | -0.8832810 | -0.5630579 |
| GOMF PROTEASOME ACTIVATING ACTIVITY | -0.6756392 | -0.6568605 | 0.5296534 | -0.2584913 |
| GOBP PROTEIN LOCALIZATION TO NUCLEAR BODY | -0.6626112 | -0.5803202 | 0.6379527 | -0.2209791 |
| GOBP COLLAGEN ACTIVATED TYROSINE KINASE RECEPTOR SIGNALING PATHWAY | 0.0273591 | 0.5198054 | -0.7764337 | -0.5899222 |
| GOBP AMP SALVAGE | -0.4390652 | -0.7894699 | 0.6290261 | -0.0928435 |
| GOBP POSITIVE REGULATION OF PYROPTOSIS | 0.5408566 | -0.4450486 | 0.7502592 | 0.4022915 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7663508 | -0.7068627 | 0.3273360 | -0.0919188 |
| GOCC SMALL RIBOSOMAL SUBUNIT | -0.6025737 | -0.7362367 | 0.5430031 | -0.0159582 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.5876682 | -0.7761913 | 0.4839422 | -0.1072468 |
#mitch_report(res=mm2,outfile="multigostratified_eos_mitchreport.html",overwrite=TRUE)
l2 <- list("crp_pod1_a"=crp_pod1_a_adj, "crp pod1 b"=crp_pod1_b_adj,
"avb crplo pod1"=avb_crplo_pod1_adj, "avb crphi pod1"=avb_crphi_pod1_adj)
m2 <- mitch_import(x=l2, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mm2 <- mitch_calc(x=m2,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm2$enrichment_result,p.adjustMANOVA<0.05),50)
top <- top[,c(1,4:7)]
rownames(top) <- top[,1]
top[,1] = NULL
colnames(top) <- gsub("^s\\.","",colnames(top))
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(as.matrix(top),trace="none",col=colfunc(25),scale="none",
margins = c(7,20), cexRow=0.6, cexCol=0.7 )
as.matrix(top) |>
kbl(caption="Top GOs in multi enrichment analysis stratified POD1") |>
kable_paper("hover", full_width = F)| crp_pod1_a | crp.pod1.b | avb.crplo.pod1 | avb.crphi.pod1 | |
|---|---|---|---|---|
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8167733 | -0.8679593 | -0.5666227 | -0.5045934 |
| GOMF LIPID ANTIGEN BINDING | -0.8167733 | -0.8679593 | -0.5666227 | -0.5045934 |
| GOMF HEMOGLOBIN BINDING | 0.4182838 | 0.9147940 | 0.3409852 | 0.8535119 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.7323194 | 0.3888329 | -0.4244698 | 0.9867404 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.8597921 | -0.4605775 | 0.8447708 | -0.0865642 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1410203 | 0.8087349 | -0.8475151 | 0.5199736 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.7613624 | -0.3541206 | 0.8623178 | 0.2544830 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | 0.7106363 | 0.2076054 | 0.8007342 | 0.5552523 |
| GOCC MCRD MEDIATED MRNA STABILITY COMPLEX | 0.5102598 | -0.8345444 | 0.6637236 | -0.3095256 |
| GOBP POSITIVE REGULATION OF CHONDROCYTE PROLIFERATION | -0.6149849 | 0.4056288 | -0.5239458 | 0.8129142 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.5482653 | 0.4020995 | -0.2221626 | 0.9748341 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.4371430 | 0.8563568 | 0.3248604 | 0.6511956 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | -0.2474953 | -0.6377133 | 0.7960490 | 0.5639381 |
| GOCC GLYCOPROTEIN IB IX V COMPLEX | 0.1345444 | 0.7311182 | -0.8314947 | 0.3584149 |
| GOCC HEMOGLOBIN COMPLEX | 0.4322177 | 0.8589747 | 0.1158029 | 0.6250435 |
| GOCC CRD MEDIATED MRNA STABILITY COMPLEX | 0.7008471 | -0.6343373 | 0.6127071 | -0.2037839 |
| GOMF HAPTOGLOBIN BINDING | 0.3746529 | 0.8515062 | 0.2412803 | 0.6111085 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | 0.9189759 | 0.0179782 | 0.5683923 | -0.3371800 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 0.8202256 | -0.0018669 | 0.6879559 | 0.3439231 |
| GOCC IGM IMMUNOGLOBULIN COMPLEX | -0.4671923 | 0.5681925 | -0.1468699 | 0.8145564 |
| GOBP LOW DENSITY LIPOPROTEIN RECEPTOR PARTICLE METABOLIC PROCESS | 0.5198224 | 0.4956308 | -0.6515743 | -0.5340676 |
| GOBP OXYGEN TRANSPORT | 0.4323212 | 0.6818717 | 0.3650238 | 0.6113920 |
| GOCC BRCA1 C COMPLEX | 0.3499788 | -0.7261731 | 0.7001302 | -0.1161105 |
| GOCC ANKYRIN 1 COMPLEX | 0.4776920 | 0.7957831 | 0.1870670 | 0.5031438 |
| GOMF INHIBITORY MHC CLASS I RECEPTOR ACTIVITY | 0.4511885 | 0.5039303 | 0.5411509 | 0.6214403 |
| GOBP NITRIC OXIDE TRANSPORT | 0.5581325 | 0.8764872 | 0.0330572 | 0.2001883 |
| GOBP MEIOTIC CYTOKINESIS | 0.5738222 | -0.4136427 | 0.7743211 | 0.1395805 |
| GOBP PLASMA CELL DIFFERENTIATION | 0.7493410 | 0.7323723 | 0.0943516 | -0.0636150 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.4684985 | 0.7325959 | 0.3863380 | 0.4201577 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.2625155 | 0.6440282 | 0.4518442 | 0.6210289 |
| GOCC SIGNAL PEPTIDASE COMPLEX | 0.3474962 | -0.7262236 | 0.6448607 | 0.0964044 |
| GOBP CARBON DIOXIDE TRANSPORT | 0.3245116 | 0.7750412 | 0.1197811 | 0.5940104 |
| GOCC MESSENGER RIBONUCLEOPROTEIN COMPLEX | 0.8082082 | -0.1839946 | 0.2727287 | -0.5535527 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.3265690 | -0.1728863 | -0.4198975 | -0.8685332 |
| GOMF SPHINGOSINE 1 PHOSPHATE RECEPTOR ACTIVITY | -0.7492099 | 0.2540983 | -0.4340716 | 0.4976264 |
| GOMF OXYGEN CARRIER ACTIVITY | 0.4090358 | 0.6685914 | 0.3030712 | 0.5897299 |
| GOBP NAIL DEVELOPMENT | -0.0788215 | 0.5531815 | 0.0564383 | 0.8462349 |
| GOBP REGULATION OF ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS | -0.5063630 | 0.6988517 | -0.3714044 | 0.3854292 |
| GOBP INTRACELLULAR GLUTAMATE HOMEOSTASIS | -0.8532944 | -0.4509224 | -0.1162274 | 0.2721197 |
| GOBP CHROMOSOME MOVEMENT TOWARDS SPINDLE POLE | 0.4279663 | 0.0454339 | 0.6502565 | 0.6389922 |
| GOBP POSITIVE REGULATION OF PROTEIN K63 LINKED UBIQUITINATION | 0.6369969 | -0.4564956 | 0.5691692 | -0.2238056 |
| GOCC MITOTIC COHESIN COMPLEX | 0.7081266 | -0.4027245 | 0.5594330 | 0.0433964 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.3476132 | 0.5611439 | 0.4853763 | 0.5536202 |
| GOBP CRD MEDIATED MRNA STABILIZATION | 0.6133597 | -0.4918420 | 0.5648072 | -0.1418350 |
| GOBP REGULATION OF VASCULAR ASSOCIATED SMOOTH MUSCLE CONTRACTION | 0.6332486 | -0.0937857 | 0.3663480 | -0.6393674 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.5404556 | -0.7443524 | 0.2458961 | 0.2028426 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.3882437 | 0.3868232 | -0.0671428 | 0.8016615 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 0.6620845 | -0.1056227 | 0.7041282 | -0.0168020 |
| GOBP ISG15 PROTEIN CONJUGATION | -0.5153355 | -0.7011500 | 0.3894667 | 0.1804490 |
| GOBP ECTODERMAL CELL DIFFERENTIATION | 0.5031299 | 0.6645801 | -0.4441254 | -0.2117005 |
#mitch_report(res=mm2,outfile="multigostratified_pod1_mitchreport.html",overwrite=TRUE)Session information
For reproducibility
sessionInfo()## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## 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=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] gtools_3.9.5 xlsx_0.6.5
## [3] DT_0.34.0 ggplot2_4.0.3
## [5] kableExtra_1.4.0 limma_3.66.0
## [7] RhpcBLASctl_0.23-42 beeswarm_0.4.0
## [9] eulerr_7.1.0 MASS_7.3-65
## [11] mitch_1.22.1 DESeq2_1.50.2
## [13] SummarizedExperiment_1.40.0 Biobase_2.70.0
## [15] MatrixGenerics_1.22.0 matrixStats_1.5.0
## [17] GenomicRanges_1.62.1 Seqinfo_1.0.0
## [19] IRanges_2.44.0 S4Vectors_0.48.1
## [21] BiocGenerics_0.56.0 generics_0.1.4
## [23] dplyr_1.2.1 WGCNA_1.74
## [25] fastcluster_1.3.0 dynamicTreeCut_1.63-1
## [27] reshape2_1.4.5 gplots_3.3.0
##
## loaded via a namespace (and not attached):
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## [4] magrittr_2.0.4 farver_2.1.2 rmarkdown_2.30
## [7] vctrs_0.7.3 base64enc_0.1-3 progress_1.2.3
## [10] htmltools_0.5.8.1 S4Arrays_1.10.1 SparseArray_1.10.10
## [13] Formula_1.2-5 sass_0.4.10 KernSmooth_2.23-26
## [16] bslib_0.9.0 htmlwidgets_1.6.4 plyr_1.8.9
## [19] echarts4r_0.5.0 impute_1.84.0 cachem_1.1.0
## [22] mime_0.13 lifecycle_1.0.5 iterators_1.0.14
## [25] pkgconfig_2.0.3 Matrix_1.7-4 R6_2.6.1
## [28] fastmap_1.2.0 shiny_1.11.1 digest_0.6.39
## [31] colorspace_2.1-2 GGally_2.4.0 textshaping_1.0.4
## [34] Hmisc_5.2-5 labeling_0.4.3 polyclip_1.10-7
## [37] abind_1.4-8 compiler_4.5.2 withr_3.0.2
## [40] doParallel_1.0.17 htmlTable_2.5.0 S7_0.2.2
## [43] backports_1.5.1 BiocParallel_1.44.0 ggstats_0.13.0
## [46] DelayedArray_0.36.1 caTools_1.18.3 tools_4.5.2
## [49] foreign_0.8-90 otel_0.2.0 httpuv_1.6.16
## [52] nnet_7.3-20 glue_1.8.0 promises_1.5.0
## [55] grid_4.5.2 polylabelr_1.0.0 checkmate_2.3.4
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## [67] pillar_1.11.1 stringr_1.6.0 later_1.4.4
## [70] rJava_1.0-18 splines_4.5.2 lattice_0.22-7
## [73] survival_3.8-3 tidyselect_1.2.1 locfit_1.5-9.12
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## [94] Rcpp_1.1.1-1.1 coda_0.19-4.1 parallel_4.5.2
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## [103] rlang_1.2.0