PADDI enrichment analysis
Mark Ziemann
2024-10-30
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")
})
load("qc.Rds")Load 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 | 0.0009787 | -0.8512143 | 0.0182266 |
| 1440 | GOBP GANGLIOSIDE CATABOLIC PROCESS | 5 | 0.0011661 | -0.8384267 | 0.0208049 |
| 9082 | GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | 5 | 0.0012744 | -0.8318774 | 0.0222287 |
| 182 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0014698 | -0.8212669 | 0.0247593 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0014698 | -0.8212669 | 0.0247593 |
| 3150 | GOBP NEUTROPHIL CLEARANCE | 6 | 0.0012737 | -0.7594524 | 0.0222287 |
| 8488 | GOMF LIPOPOLYSACCHARIDE IMMUNE RECEPTOR ACTIVITY | 6 | 0.0021051 | -0.7248445 | 0.0326569 |
| 4418 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0000734 | -0.6902961 | 0.0023749 |
| 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 | 0.0017325 | -0.6836665 | 0.0280229 |
| 6322 | GOBP SPHINGOMYELIN BIOSYNTHETIC PROCESS | 10 | 0.0001968 | -0.6798170 | 0.0051157 |
| 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 | 0.0004428 | 0.6415096 | 0.0099987 |
| 1521 | GOBP GLYCOLIPID CATABOLIC PROCESS | 16 | 0.0000097 | -0.6386645 | 0.0004357 |
| 264 | GOBP AUTOPHAGIC CELL DEATH | 8 | 0.0018456 | -0.6357264 | 0.0294453 |
| 7329 | GOCC MYOSIN FILAMENT | 12 | 0.0001847 | 0.6232958 | 0.0049748 |
| 7390 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0001087 | -0.6198648 | 0.0032154 |
| 446 | GOBP CARDIAC NEURAL CREST CELL DIFFERENTIATION INVOLVED IN HEART DEVELOPMENT | 9 | 0.0013385 | -0.6173907 | 0.0231310 |
| 1444 | GOBP GASTRO INTESTINAL SYSTEM SMOOTH MUSCLE CONTRACTION | 9 | 0.0014233 | -0.6139853 | 0.0241927 |
| 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 | 0.0030503 | 0.6048280 | 0.0429503 |
| 1774 | GOBP INTERLEUKIN 33 MEDIATED SIGNALING PATHWAY | 8 | 0.0031017 | -0.6037760 | 0.0434103 |
| 1961 | GOBP LOCOMOTION INVOLVED IN LOCOMOTORY BEHAVIOR | 10 | 0.0011398 | -0.5941080 | 0.0205717 |
| 7620 | GOCC SPECTRIN ASSOCIATED CYTOSKELETON | 8 | 0.0036748 | 0.5930267 | 0.0497185 |
| 4362 | GOBP PROGESTERONE RECEPTOR SIGNALING PATHWAY | 9 | 0.0021035 | -0.5919166 | 0.0326569 |
| 872 | GOBP CRD MEDIATED MRNA STABILIZATION | 10 | 0.0012884 | -0.5877219 | 0.0224310 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/crp_t0_adj_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac3aa68d80.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- crp_eos_adj
myname <- "crp_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0049106 |
| 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 | -0.8614971 | 0.0000000 |
| 257 | GOBP ATRIOVENTRICULAR NODE DEVELOPMENT | 5 | 0.0008930 | 0.8578340 | 0.0122641 |
| 8838 | GOMF PEROXIREDOXIN ACTIVITY | 8 | 0.0000390 | -0.8397185 | 0.0009084 |
| 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 | -0.8313274 | 0.0004192 |
| 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 | -0.8122820 | 0.0000000 |
| 7264 | GOCC LARGE RIBOSOMAL SUBUNIT | 110 | 0.0000000 | -0.8076518 | 0.0000000 |
| 7428 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000005 | -0.8075069 | 0.0000184 |
| 7275 | GOCC LSM1 7 PAT1 COMPLEX | 5 | 0.0019820 | -0.7986360 | 0.0228292 |
| 4434 | GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 6 | 0.0007252 | 0.7966929 | 0.0106015 |
| 9237 | GOMF THIOREDOXIN DEPENDENT PEROXIREDOXIN ACTIVITY | 6 | 0.0007726 | -0.7925855 | 0.0110481 |
| 7699 | GOCC TOM COMPLEX | 7 | 0.0002815 | -0.7925739 | 0.0049808 |
| 2809 | GOBP NEGATIVE REGULATION OF MESENCHYMAL CELL PROLIFERATION | 5 | 0.0021516 | -0.7923252 | 0.0242016 |
| 7333 | GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | 32 | 0.0000000 | -0.7910303 | 0.0000000 |
| 7581 | GOCC RIBOSOMAL SUBUNIT | 182 | 0.0000000 | -0.7898529 | 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 | 0.0024478 | -0.7823225 | 0.0266267 |
| 6235 | GOBP SEQUESTERING OF IRON ION | 5 | 0.0024495 | -0.7822679 | 0.0266267 |
| 7537 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000193 | -0.7802447 | 0.0005048 |
| 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/Rtmpadl22y/crp_eos_adj_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac33aa29c8.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.0102542 |
| 8370 | GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | 5 | 0.0009517 | 0.8532380 | 0.0107183 |
| 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 | 0.0184112 |
| 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 | 0.0026129 | 0.7772214 | 0.0232753 |
| 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 | 0.7715580 | 0.0025565 |
| 4884 | GOBP REGULATION OF CILIUM BEAT FREQUENCY INVOLVED IN CILIARY MOTILITY | 7 | 0.0004350 | -0.7677277 | 0.0058656 |
| 8611 | GOMF NEUROTROPHIN BINDING | 7 | 0.0004796 | 0.7620527 | 0.0063209 |
| 6706 | GOBP VIRAL TRANSLATIONAL TERMINATION REINITIATION | 5 | 0.0032873 | -0.7590361 | 0.0276900 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0002184 | 0.7546482 | 0.0033824 |
| 1200 | GOBP EOSINOPHIL DIFFERENTIATION | 5 | 0.0037032 | 0.7494541 | 0.0301967 |
| 8407 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0037075 | -0.7493599 | 0.0301967 |
| 5025 | GOBP REGULATION OF FEVER GENERATION | 8 | 0.0002590 | 0.7457637 | 0.0038881 |
| 6137 | GOBP SA NODE CELL TO ATRIAL CARDIAC MUSCLE CELL SIGNALING | 5 | 0.0042908 | 0.7374623 | 0.0332629 |
| 7055 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | 7 | 0.0008381 | -0.7288901 | 0.0097827 |
| 828 | GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 11 | 0.0000292 | 0.7276665 | 0.0006671 |
| 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 | 0.0378928 |
| 1484 | GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | 5 | 0.0052750 | -0.7203690 | 0.0385908 |
| 1098 | GOBP ECTODERMAL CELL DIFFERENTIATION | 6 | 0.0023216 | 0.7179366 | 0.0213355 |
| 6536 | GOBP TRNA SURVEILLANCE | 8 | 0.0004627 | -0.7148035 | 0.0061595 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/crp_pod1_adj_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac35becb4d3.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEMulti-contrast enrichment analysis.
l1 <- list("crp_t0_adj"=crp_t0_adj,"crp_eos_adj"=crp_eos_adj,
"crp_pod1_adj"=crp_pod1_adj,"avb_t0_adj"=avb_t0_adj,
"avb_eos_adj"=avb_eos_adj,"avb_pod1_adj"=avb_pod1_adj)
m1 <- mitch_import(x=l1, DEtype="deseq2", geneTable=gt )## Note: Mean no. genes in input = 21771.6666666667## Note: no. genes in output = 21032## Note: estimated proportion of input genes in output = 0.966mm1 <- mitch_calc(x=m1,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- head(subset (mm1$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 | -0.5591573 | -0.8345365 | -0.8455129 |
| GOMF LIPID ANTIGEN BINDING | -0.8195083 | -0.9451372 | -0.9618395 | -0.5591573 | -0.8345365 | -0.8455129 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.6124982 | -0.2161316 | 0.8558805 | -0.6377229 | -0.9498169 | 0.3278927 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.8496600 | -0.7733010 | 0.3139107 | 0.0278975 | -0.6641651 | 0.7488372 |
| GOMF UNMETHYLATED CPG BINDING | 0.6475978 | 0.6992769 | 0.3655504 | 0.8642850 | 0.5636857 | 0.0763200 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6812230 | -0.6814405 | -0.5741125 | -0.2838729 | -0.6884118 | -0.4528690 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | -0.2951158 | -0.2606649 | 0.7804347 | 0.4466923 | -0.4260142 | 0.9093737 |
| GOMF GUANYLATE CYCLASE ACTIVITY | -0.5090312 | -0.6607410 | 0.3116279 | -0.4641176 | -0.5910972 | 0.7271698 |
| GOCC SIGNAL PEPTIDASE COMPLEX | -0.7335616 | -0.7559899 | -0.3328007 | -0.3376135 | -0.4300281 | 0.5274266 |
| GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | -0.8301422 | -0.6714890 | 0.1712560 | -0.7427308 | -0.1596709 | 0.2062016 |
| GOBP SIALYLATION | 0.3437014 | 0.4938806 | 0.5696915 | 0.6637814 | 0.4600812 | 0.6473255 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.3886527 | -0.9377182 | -0.7479812 | -0.0976744 | -0.1264755 | -0.3362058 |
| GOMF NEUROTROPHIN BINDING | -0.1025786 | -0.2528351 | 0.7653813 | -0.4807950 | -0.7916494 | 0.4336674 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.8368384 | -0.6641461 | -0.3526038 | -0.5252390 | 0.0558425 | -0.3900224 |
| GOBP VIRAL TRANSLATIONAL TERMINATION REINITIATION | -0.2735816 | -0.8137252 | -0.7576640 | 0.0841490 | -0.2414515 | -0.5572740 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.1578522 | -0.1842956 | 0.7847903 | -0.4801199 | -0.7664320 | 0.4257744 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.4704400 | -0.8306914 | -0.7273722 | -0.1266995 | -0.2572380 | -0.3604213 |
| GOMF PHOSPHATIDYLETHANOLAMINE FLIPPASE ACTIVITY | 0.3079374 | 0.6164931 | 0.6903029 | 0.4821325 | -0.1484092 | 0.6624911 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.2149878 | -0.5646977 | -0.0063731 | -0.6123054 | -0.9256001 | -0.1832018 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.3432893 | -0.7126098 | -0.7076001 | 0.0958337 | 0.4385681 | -0.5294873 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.2409173 | -0.8751282 | -0.0402174 | 0.1710277 | -0.7545915 | 0.4175098 |
| GOMF PROTEIN PHOSPHATASE 2B BINDING | 0.0594949 | 0.2991677 | 0.4860893 | 0.4945927 | 0.6330623 | 0.7859894 |
| GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | -0.6102463 | -0.7501206 | -0.2286326 | -0.3976151 | -0.1330457 | 0.6278036 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5152034 | 0.2091855 | -0.3362662 | -0.6811567 | -0.0696281 | -0.8103935 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.5645979 | -0.5993342 | -0.7188187 | 0.0256908 | 0.5512627 | -0.2090550 |
| GOCC BOX C D RNP COMPLEX | 0.0616446 | -0.7772959 | -0.7209302 | 0.0223998 | -0.1807676 | -0.5995054 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | -0.1202955 | 0.3730619 | 0.6816323 | 0.3878848 | 0.2459970 | 0.8213165 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.2252188 | 0.6751213 | 0.7736396 | -0.0417856 | -0.1560597 | 0.6020738 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | -0.1169829 | 0.3041328 | 0.6638798 | -0.2045846 | -0.6587055 | 0.6565749 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | -0.3607432 | -0.5272606 | 0.5447929 | 0.2692848 | -0.5830663 | 0.5760344 |
| GOBP REGULATION OF NITRIC OXIDE MEDIATED SIGNAL TRANSDUCTION | -0.3685262 | -0.5333619 | 0.5008513 | -0.4894374 | -0.7059590 | -0.1571979 |
| GOMF HEMOGLOBIN BINDING | 0.3354850 | 0.3375505 | 0.7282147 | 0.4291286 | 0.1136402 | 0.6857890 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | -0.1038379 | 0.3929519 | 0.3945879 | -0.7768393 | -0.6404813 | -0.2717934 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | -0.4757126 | 0.4970613 | 0.4756311 | 0.4296857 | 0.2183183 | 0.6848106 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.6166911 | -0.8033647 | -0.0895051 | 0.1710211 | -0.4075763 | 0.4093403 |
| GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 0.5256531 | 0.5234245 | 0.2710447 | 0.6996093 | 0.0689180 | 0.5194021 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.1479949 | 0.5753857 | 0.7302265 | -0.0238852 | -0.0136963 | 0.7044514 |
| GOCC MHC CLASS II PROTEIN COMPLEX | 0.0425402 | -0.4505083 | -0.6705524 | 0.2887535 | 0.5916195 | -0.5404736 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.2550708 | -0.8757828 | -0.6899245 | -0.0975709 | -0.0089352 | -0.2354403 |
| GOCC TOM COMPLEX | -0.4091931 | -0.7891490 | -0.6323832 | -0.3023815 | -0.2649703 | -0.0614167 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | -0.5549320 | 0.0041219 | 0.4822918 | -0.0905546 | -0.3096008 | 0.8317480 |
| GOBP REGULATION OF MONOATOMIC ANION TRANSMEMBRANE TRANSPORT | 0.1604318 | 0.6618443 | 0.1336662 | 0.6289723 | 0.4798687 | 0.4720502 |
| GOMF RETROMER COMPLEX BINDING | -0.6824325 | -0.4221250 | 0.2937576 | -0.2049977 | -0.6599386 | 0.3404050 |
| GOCC ARP2 3 PROTEIN COMPLEX | -0.5179248 | -0.3225409 | 0.4729370 | -0.0001110 | -0.4788671 | 0.7026326 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | -0.6876630 | -0.2458105 | 0.4853718 | 0.0278639 | -0.4554017 | 0.5729725 |
| GOCC F ACTIN CAPPING PROTEIN COMPLEX | -0.3607066 | -0.2261457 | 0.6854629 | -0.1692747 | -0.3227246 | 0.7195583 |
| GOBP NEGATIVE REGULATION OF BLOOD VESSEL ENDOTHELIAL CELL PROLIFERATION INVOLVED IN SPROUTING ANGIOGENESIS | -0.1781614 | -0.3327056 | 0.6307795 | -0.5678889 | -0.6120226 | -0.2191183 |
| GOBP PEPTIDE ANTIGEN ASSEMBLY WITH MHC CLASS II PROTEIN COMPLEX | 0.0406658 | -0.4428177 | -0.6487704 | 0.2658130 | 0.5703071 | -0.5146405 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.3719997 | 0.0930435 | 0.7152890 | 0.1751165 | 0.0257935 | 0.7598846 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.4250440 | -0.5229562 | -0.8566224 | 0.0188805 | 0.2804109 | 0.0031864 |
mitch_report(res=mm1,outfile="multigo_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/Rtmpadl22y/multigo_all_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac31600e73e.html##
## Output created: /tmp/Rtmpadl22y/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 | -0.8318774 | -0.7390899 |
| GOMF UNMETHYLATED CPG BINDING | 0.6415096 | 0.8656084 |
| GOCC ATP BINDING CASSETTE ABC TRANSPORTER COMPLEX | 0.7081546 | 0.7853190 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8212669 | -0.5548319 |
| GOMF LIPID ANTIGEN BINDING | -0.8212669 | -0.5548319 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.8384267 | -0.5206220 |
| GOCC MPP7 DLG1 LIN7 COMPLEX | -0.6430826 | -0.6931169 |
| GOCC TORC1 COMPLEX | 0.5450665 | 0.7102543 |
| GOBP NOTOCHORD MORPHOGENESIS | 0.5957685 | 0.6518711 |
| GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 0.5195405 | 0.7026810 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.8512143 | 0.0335788 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5112361 | -0.6775826 |
| GOMF FATTY ACYL COA SYNTHASE ACTIVITY | -0.0991082 | -0.7903316 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | -0.1110176 | -0.7738120 |
| GOBP MITOTIC SPINDLE ELONGATION | 0.2121406 | 0.7466656 |
| GOMF GABA A RECEPTOR ACTIVITY | 0.1665584 | -0.7553716 |
| GOBP LEUKOCYTE ADHESION TO ARTERIAL ENDOTHELIAL CELL | -0.0647153 | -0.7660553 |
| GOBP NEUTROPHIL CLEARANCE | -0.7594524 | -0.0740792 |
| GOMF LIPOPOLYSACCHARIDE IMMUNE RECEPTOR ACTIVITY | -0.7248445 | -0.2255763 |
| GOBP PROTEIN DEMETHYLATION | 0.2149897 | 0.7268195 |
| GOMF HAPTOGLOBIN BINDING | 0.6048280 | 0.4521201 |
| GOBP REGULATION OF TRANSLATION INITIATION IN RESPONSE TO ENDOPLASMIC RETICULUM STRESS | -0.6583798 | -0.3691794 |
| GOCC MYOSIN FILAMENT | 0.6232958 | 0.4185272 |
| GOMF SERINE TYPE EXOPEPTIDASE ACTIVITY | -0.5735316 | -0.4828820 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6836665 | -0.2798008 |
| GOCC NETWORK FORMING COLLAGEN TRIMER | -0.0551592 | -0.7358367 |
| GOBP TELOMERE MAINTENANCE VIA SEMI CONSERVATIVE REPLICATION | 0.2231828 | 0.6983466 |
| GOBP SPHINGOMYELIN BIOSYNTHETIC PROCESS | -0.6798170 | -0.2715462 |
| GOBP GASTRO INTESTINAL SYSTEM SMOOTH MUSCLE CONTRACTION | -0.6139853 | -0.3811913 |
| GOBP SPINDLE ELONGATION | 0.1563625 | 0.7052942 |
| GOBP REGULATION OF CDC42 PROTEIN SIGNAL TRANSDUCTION | -0.2932449 | 0.6580837 |
| GOBP POSITIVE REGULATION OF FEVER GENERATION | -0.2542913 | -0.6707941 |
| GOBP GLYCOLIPID CATABOLIC PROCESS | -0.6386645 | -0.3250378 |
| GOMF RETROMER COMPLEX BINDING | -0.6856401 | -0.1997825 |
| GOMF DNA TOPOISOMERASE ACTIVITY | 0.0779516 | 0.7076625 |
| GOBP NOTOCHORD DEVELOPMENT | 0.4573962 | 0.5419105 |
| GOBP PARTURITION | -0.5110247 | -0.4842360 |
| GOBP SPINDLE MIDZONE ASSEMBLY | 0.0588616 | 0.6988467 |
| GOBP BASE EXCISION REPAIR GAP FILLING | 0.2277505 | 0.6624333 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | -0.6902961 | 0.0337078 |
| GOBP MRNA 3 SPLICE SITE RECOGNITION | 0.0212526 | 0.6902366 |
| GOCC HEMOGLOBIN COMPLEX | 0.5499085 | 0.4135590 |
| GOBP REGULATION OF DNA TEMPLATED DNA REPLICATION INITIATION | 0.2438363 | 0.6396870 |
| GOBP REGULATION OF FEVER GENERATION | -0.1812734 | -0.6601180 |
| GOCC GABA RECEPTOR COMPLEX | 0.2953104 | -0.6111264 |
| GOMF GABA RECEPTOR ACTIVITY | 0.2953104 | -0.6111264 |
| GOBP NEGATIVE REGULATION OF PROTEIN LOCALIZATION TO CELL SURFACE | -0.5050011 | -0.4426510 |
| GOMF SULFATIDE BINDING | -0.5304642 | 0.4108209 |
| GOMF ANKYRIN REPEAT BINDING | -0.0348518 | 0.6656604 |
| GOCC CORVET COMPLEX | -0.3793559 | 0.5469057 |
mitch_report(res=mm1,outfile="multigo_t0_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/multigo_t0_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac332094e31.html##
## Output created: /tmp/Rtmpadl22y/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 | -0.8317541 |
| GOMF LIPID ANTIGEN BINDING | -0.9463490 | -0.8317541 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7775939 | -0.6580158 |
| GOBP REGULATION OF CALCIUM ION EXPORT ACROSS PLASMA MEMBRANE | -0.7517141 | -0.6733473 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.5292896 | -0.8568635 |
| GOBP ATRIOVENTRICULAR NODE DEVELOPMENT | 0.8578340 | 0.5096845 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX CIRCULATING | -0.6083114 | -0.7686642 |
| GOBP POSITIVE REGULATION OF SYNAPTIC VESICLE ENDOCYTOSIS | -0.5194326 | -0.8270437 |
| GOBP POSITIVE REGULATION OF SYNAPTIC VESICLE RECYCLING | -0.5775737 | -0.7865198 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.2197872 | -0.9491134 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.6843917 | -0.6834693 |
| GOMF C PALMITOYLTRANSFERASE ACTIVITY | -0.4776212 | -0.8370283 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.3957543 | -0.8659642 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.9390015 | -0.1156133 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.7717222 | -0.5135634 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8837137 | -0.2706556 |
| GOMF NUCLEASE INHIBITOR ACTIVITY | -0.8195183 | -0.4085845 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.5323935 | -0.7319893 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | 0.1789579 | 0.8841866 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.8075069 | -0.4007305 |
| GOMF UNMETHYLATED CPG BINDING | 0.6967302 | 0.5711674 |
| GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 0.7966929 | -0.4051137 |
| GOMF 5S RRNA BINDING | -0.8313274 | -0.3025213 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8335864 | -0.2639862 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.8343683 | -0.2470509 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8361272 | -0.2236664 |
| GOCC ENDOPLASMIC RETICULUM PALMITOYLTRANSFERASE COMPLEX | -0.5337297 | -0.6766859 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8614971 | 0.0114741 |
| GOMF PEROXIREDOXIN ACTIVITY | -0.8397185 | -0.1768564 |
| 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 | -0.2558853 |
| GOCC INTRACILIARY TRANSPORT PARTICLE A | 0.2346755 | 0.7911987 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.6024007 | 0.5604438 |
| GOCC COLLAGEN TYPE IV TRIMER | 0.3771574 | -0.7287260 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | -0.7705189 | -0.2743429 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.8161184 | -0.0134202 |
| GOBP THYROID HORMONE TRANSPORT | -0.6597854 | -0.4796809 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.8122820 | -0.0204296 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7777734 | -0.2246142 |
| GOCC LARGE RIBOSOMAL SUBUNIT | -0.8076518 | -0.0530827 |
| GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | -0.7853563 | -0.1677930 |
| GOCC MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX III | -0.7597162 | -0.2517103 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 0.4488398 | -0.6593613 |
| GOBP PROTEIN LOCALIZATION TO CENP A CONTAINING CHROMATIN | -0.6379465 | -0.4776515 |
| GOMF THIOREDOXIN DEPENDENT PEROXIREDOXIN ACTIVITY | -0.7925855 | -0.0765698 |
| GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | -0.7910303 | -0.0640791 |
| GOCC RIBOSOMAL SUBUNIT | -0.7898529 | -0.0392974 |
| GOCC RESPIRATORY CHAIN COMPLEX IV | -0.7185268 | -0.3235771 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | -0.5336547 | -0.5781749 |
mitch_report(res=mm1,outfile="multigo_eos_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/multigo_eos_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac34c54c555.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.7772214 | 0.9094691 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 0.6787782 | 0.8214493 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.7127124 | 0.7600289 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.7276665 | 0.7045048 |
| GOMF HEMOGLOBIN BINDING | 0.7251113 | 0.6859106 |
| GOCC F ACTIN CAPPING PROTEIN COMPLEX | 0.6820645 | 0.7195707 |
| GOBP N ACYLPHOSPHATIDYLETHANOLAMINE METABOLIC PROCESS | -0.7922687 | -0.5935740 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.7715580 | 0.6020828 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.4787029 | 0.8318508 |
| 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 | 0.8532380 | 0.3278614 |
| GOBP MEIOTIC CYTOKINESIS | 0.4106776 | 0.8011798 |
| GOBP NEGATIVE REGULATION OF DELAYED RECTIFIER POTASSIUM CHANNEL ACTIVITY | 0.6183349 | 0.6537432 |
| GOBP REGULATION OF CILIUM BEAT FREQUENCY INVOLVED IN CILIARY MOTILITY | -0.7677277 | -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 | -0.7091197 | -0.5297846 |
| GOMF NEUROTROPHIN BINDING | 0.7620527 | 0.4337489 |
| GOCC UBIQUINONE BIOSYNTHESIS COMPLEX | -0.8169781 | -0.3055804 |
| GOBP DENDRITIC CELL APOPTOTIC PROCESS | 0.6379004 | 0.5913617 |
| 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 | 0.6396682 |
| GOBP PLASMA CELL DIFFERENTIATION | 0.7546482 | 0.3834196 |
| GOBP INTESTINAL CHOLESTEROL ABSORPTION | 0.6864755 | 0.4940263 |
| GOCC ARP2 3 PROTEIN COMPLEX | 0.4687964 | 0.7028704 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.4712416 | 0.6849155 |
| GOBP PEPTIDE ANTIGEN ASSEMBLY WITH MHC CLASS II PROTEIN COMPLEX | -0.6502862 | -0.5147740 |
| GOBP DETOXIFICATION OF INORGANIC COMPOUND | 0.5633523 | 0.6075514 |
| GOMF BETA 2 MICROGLOBULIN BINDING | -0.6712484 | -0.4852612 |
| GOBP ISG15 PROTEIN CONJUGATION | -0.8159113 | 0.1156242 |
| GOCC MHC PROTEIN COMPLEX | -0.6731614 | -0.4734359 |
| 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 | -0.1784269 |
| GOCC CYTOLYTIC GRANULE | 0.4785603 | 0.6330672 |
| GOMF GLUCOSE BINDING | 0.6274448 | 0.4856673 |
| GOCC ENDOPLASMIC RETICULUM CHAPERONE COMPLEX | 0.5418853 | 0.5760885 |
| GOBP NEGATIVE REGULATION OF T CELL MEDIATED CYTOTOXICITY | 0.5268625 | 0.5853156 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | -0.2465540 | 0.7362462 |
| GOBP LIPID DIGESTION | 0.6421465 | 0.4325126 |
| GOBP HYPOTONIC RESPONSE | 0.5281363 | 0.5653250 |
| GOBP U4 SNRNA 3 END PROCESSING | -0.7092492 | -0.3065663 |
| GOBP REGULATION OF CD8 POSITIVE ALPHA BETA T CELL DIFFERENTIATION | 0.6276653 | 0.4315251 |
| GOBP RRNA 3 END PROCESSING | -0.6953538 | -0.3106341 |
mitch_report(res=mm1,outfile="multigo_eos_mitchreport.html",overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/multigo_eos_mitchreport.rds ".##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac35b8b46a0.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.0017540 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0001523 | -0.9778642 | 0.0017540 |
| 2070 | GOBP MAINTENANCE OF PROTEIN LOCATION IN MITOCHONDRION | 5 | 0.0003746 | -0.9185365 | 0.0038482 |
| 8458 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0004959 | -0.8993277 | 0.0048596 |
| 7513 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0009132 | -0.8562268 | 0.0080997 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0001252 | -0.8370633 | 0.0014686 |
| 189 | GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | 7 | 0.0001266 | -0.8364491 | 0.0014818 |
| 7294 | GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 10 | 0.0000058 | -0.8278591 | 0.0000981 |
| 7012 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 52 | 0.0000000 | -0.8206756 | 0.0000000 |
| 2203 | GOBP METHYLGLYOXAL METABOLIC PROCESS | 6 | 0.0005354 | -0.8161361 | 0.0051659 |
| 6205 | GOBP SEQUESTERING OF IRON ION | 5 | 0.0016207 | -0.8139309 | 0.0129947 |
| 7500 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000116 | -0.8006679 | 0.0001830 |
| 4988 | GOBP REGULATION OF ELECTRON TRANSFER ACTIVITY | 5 | 0.0020454 | -0.7962223 | 0.0157127 |
| 1522 | GOBP GLYCOLIPID TRANSPORT | 8 | 0.0001004 | -0.7940376 | 0.0012076 |
| 8723 | GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | 5 | 0.0021990 | -0.7906426 | 0.0167146 |
| 8228 | GOMF GABA A RECEPTOR ACTIVITY | 5 | 0.0022262 | 0.7896913 | 0.0168800 |
| 8429 | GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | 6 | 0.0009554 | -0.7786620 | 0.0083932 |
| 8901 | GOMF PORIN ACTIVITY | 6 | 0.0009602 | -0.7783266 | 0.0084134 |
| 7390 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000012 | -0.7767024 | 0.0000250 |
| 7814 | GOMF ADP RIBOSE DIPHOSPHATASE ACTIVITY | 6 | 0.0009912 | -0.7762227 | 0.0086205 |
| 7711 | GOCC U7 SNRNP | 7 | 0.0003785 | -0.7757464 | 0.0038797 |
| 2252 | GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | 14 | 0.0000006 | -0.7704782 | 0.0000130 |
| 1849 | GOBP ISOCITRATE METABOLIC PROCESS | 6 | 0.0010827 | -0.7703531 | 0.0092953 |
| 96 | GOBP ALDEHYDE CATABOLIC PROCESS | 10 | 0.0000246 | -0.7702379 | 0.0003544 |
| 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 | -0.7598094 | 0.0000403 |
| 6206 | GOBP SEQUESTERING OF METAL ION | 8 | 0.0002028 | -0.7584850 | 0.0022450 |
| 8438 | GOMF ISOCITRATE DEHYDROGENASE NAD P PLUS ACTIVITY | 5 | 0.0033527 | -0.7574571 | 0.0233389 |
| 9294 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0000831 | -0.7574066 | 0.0010318 |
| 7512 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | 21 | 0.0000000 | -0.7549327 | 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/Rtmpadl22y/crp_t0_a_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac3486ceb5d.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.0005569 | -0.8136358 | 0.0416543 |
| 1270 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0001930 | -0.8135663 | 0.0210836 |
| 3198 | GOBP NUCLEAR PORE ORGANIZATION | 15 | 0.0000043 | -0.6849417 | 0.0010987 |
| 3196 | GOBP NUCLEAR PORE COMPLEX ASSEMBLY | 11 | 0.0001520 | -0.6594704 | 0.0182928 |
| 7173 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0003294 | 0.6557182 | 0.0279949 |
| 4130 | GOBP POSITIVE REGULATION OF PROTEIN POLYUBIQUITINATION | 16 | 0.0000082 | -0.6437151 | 0.0018784 |
| 4418 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0002661 | -0.6348248 | 0.0239851 |
| 9025 | GOMF RIBOSOMAL LARGE SUBUNIT BINDING | 14 | 0.0002643 | -0.5630164 | 0.0239851 |
| 7333 | GOCC NADPH OXIDASE COMPLEX | 14 | 0.0004743 | 0.5394008 | 0.0369492 |
| 3168 | GOBP NLS BEARING PROTEIN IMPORT INTO NUCLEUS | 19 | 0.0002668 | -0.4830298 | 0.0239851 |
| 6506 | GOBP TOOTH MINERALIZATION | 19 | 0.0006462 | 0.4520207 | 0.0464692 |
| 1047 | GOBP DNA DOUBLE STRAND BREAK PROCESSING | 20 | 0.0005833 | -0.4441739 | 0.0432818 |
| 2301 | GOBP MITOTIC SISTER CHROMATID COHESION | 31 | 0.0001526 | -0.3929062 | 0.0182928 |
| 8239 | GOMF GDP BINDING | 63 | 0.0000047 | -0.3332649 | 0.0011668 |
| 8289 | GOMF G PROTEIN ACTIVITY | 41 | 0.0002569 | -0.3298666 | 0.0239851 |
| 2738 | GOBP NEGATIVE REGULATION OF INTRACELLULAR TRANSPORT | 39 | 0.0005207 | -0.3210502 | 0.0395782 |
| 4953 | GOBP REGULATION OF DENDRITIC SPINE DEVELOPMENT | 50 | 0.0002233 | -0.3016939 | 0.0219722 |
| 7189 | GOCC IMMUNOGLOBULIN COMPLEX | 112 | 0.0000001 | 0.2980439 | 0.0000335 |
| 196 | GOBP ANTIMICROBIAL HUMORAL IMMUNE RESPONSE MEDIATED BY ANTIMICROBIAL PEPTIDE | 53 | 0.0002793 | 0.2884967 | 0.0241817 |
| 7700 | GOCC T CELL RECEPTOR COMPLEX | 123 | 0.0000001 | 0.2837633 | 0.0000338 |
| 259 | GOBP ATTACHMENT OF SPINDLE MICROTUBULES TO KINETOCHORE | 52 | 0.0004013 | -0.2836790 | 0.0329087 |
| 8151 | GOMF DOUBLE STRANDED RNA BINDING | 70 | 0.0002167 | -0.2556199 | 0.0217832 |
| 7149 | GOCC GOLGI ASSOCIATED VESICLE | 80 | 0.0001612 | -0.2439812 | 0.0188329 |
| 197 | GOBP ANTIMICROBIAL HUMORAL RESPONSE | 83 | 0.0001454 | 0.2411757 | 0.0182928 |
| 7888 | GOMF ATP DEPENDENT ACTIVITY ACTING ON RNA | 72 | 0.0004884 | -0.2376352 | 0.0377356 |
| 9028 | GOMF RIBOSOME BINDING | 101 | 0.0000567 | -0.2317943 | 0.0093050 |
| 820 | GOBP COLLAGEN METABOLIC PROCESS | 76 | 0.0005057 | 0.2306997 | 0.0387533 |
| 4408 | GOBP PROTEIN DEUBIQUITINATION | 82 | 0.0003579 | -0.2279796 | 0.0298751 |
| 9302 | GOMF UBIQUITIN LIKE PROTEIN PEPTIDASE ACTIVITY | 106 | 0.0000655 | -0.2243726 | 0.0103851 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/crp_t0_b_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac36a037eb3.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- crp_eos_a_adj
myname <- "crp_eos_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | -0.8540725 | 0.0001711 |
| 7551 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | 13 | 0.0000002 | -0.8317951 | 0.0000148 |
| 183 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0013563 | -0.8272620 | 0.0298666 |
| 8512 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0013563 | -0.8272620 | 0.0298666 |
| 8491 | GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | 5 | 0.0014406 | -0.8227698 | 0.0314277 |
| 7222 | GOCC IGE IMMUNOGLOBULIN COMPLEX | 5 | 0.0018881 | -0.8023461 | 0.0379287 |
| 7550 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0020772 | -0.7950350 | 0.0405966 |
| 4252 | GOBP POSITIVE REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY | 15 | 0.0000001 | -0.7832545 | 0.0000111 |
| 6601 | GOBP TRNA THIO MODIFICATION | 5 | 0.0024217 | -0.7831590 | 0.0451338 |
| 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 | 0.0001318 | -0.7804443 | 0.0046129 |
| 6806 | GOBP XMP METABOLIC PROCESS | 7 | 0.0004016 | -0.7723328 | 0.0117008 |
| 7699 | GOCC TOM COMPLEX | 7 | 0.0004352 | -0.7676947 | 0.0124855 |
| 8932 | GOMF PORIN ACTIVITY | 6 | 0.0011441 | -0.7666682 | 0.0265371 |
| 7549 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | 21 | 0.0000000 | -0.7663074 | 0.0000001 |
| 4817 | GOBP REGULATION OF CALCIUM IMPORT INTO THE MITOCHONDRION | 6 | 0.0015052 | -0.7481017 | 0.0322384 |
| 7223 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 11 | 0.0000194 | -0.7437445 | 0.0009223 |
| 6663 | GOBP U4 SNRNA 3 END PROCESSING | 8 | 0.0002735 | -0.7429176 | 0.0086963 |
| 3366 | GOBP OXALOACETATE METABOLIC PROCESS | 7 | 0.0006643 | -0.7428545 | 0.0176132 |
| 4530 | GOBP PROTEIN MATURATION BY 4FE 4S CLUSTER TRANSFER | 8 | 0.0002886 | -0.7400755 | 0.0090862 |
| 7249 | GOCC IRON SULFUR CLUSTER ASSEMBLY COMPLEX | 12 | 0.0000102 | -0.7357226 | 0.0005310 |
| 7428 | GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | 13 | 0.0000044 | -0.7355730 | 0.0002482 |
| 1 | GOBP 2FE 2S CLUSTER ASSEMBLY | 11 | 0.0000251 | -0.7336729 | 0.0011528 |
| 2278 | GOBP MITOCHONDRIAL RIBOSOME ASSEMBLY | 12 | 0.0000115 | -0.7311214 | 0.0005848 |
| 9326 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0001531 | -0.7286848 | 0.0052610 |
| 7326 | GOCC MITOCHONDRIAL INTERMEMBRANE SPACE PROTEIN TRANSPORTER COMPLEX | 6 | 0.0019976 | -0.7285197 | 0.0394520 |
| 7718 | GOCC TRANSLOCON COMPLEX | 6 | 0.0020089 | -0.7281256 | 0.0395914 |
| 7419 | GOCC NUCLEOLAR EXOSOME RNASE COMPLEX | 10 | 0.0000776 | -0.7215517 | 0.0029799 |
| 9320 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0009618 | -0.7205088 | 0.0234344 |
| 4531 | GOBP PROTEIN MATURATION BY IRON SULFUR CLUSTER TRANSFER | 17 | 0.0000004 | -0.7105439 | 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/Rtmpadl22y/crp_eos_a_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac31a3b1467.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.0064528 |
| 7048 | GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 53 | 0.0000000 | -0.8656617 | 0.0000000 |
| 8371 | GOMF HISTONE H3K4ME H3K4ME2 H3K4ME3 DEMETHYLASE ACTIVITY | 5 | 0.0009202 | 0.8556697 | 0.0134416 |
| 7537 | GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | 10 | 0.0000062 | -0.8248761 | 0.0002014 |
| 7550 | GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | 5 | 0.0015189 | -0.8188051 | 0.0193078 |
| 7535 | GOCC PROTEASOME CORE COMPLEX | 18 | 0.0000000 | -0.7956467 | 0.0000003 |
| 146 | GOBP AMP SALVAGE | 5 | 0.0022321 | -0.7894880 | 0.0255668 |
| 7751 | GOCC UNIPLEX COMPLEX | 6 | 0.0009791 | -0.7770351 | 0.0140880 |
| 7125 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | 7 | 0.0003752 | -0.7762433 | 0.0066916 |
| 9186 | GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | 158 | 0.0000000 | -0.7703332 | 0.0000000 |
| 7536 | GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | 7 | 0.0004760 | -0.7624981 | 0.0080740 |
| 6253 | GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | 6 | 0.0012190 | -0.7624093 | 0.0164071 |
| 9326 | GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | 9 | 0.0000754 | -0.7619019 | 0.0017723 |
| 1796 | GOBP INTERNEURON MIGRATION | 5 | 0.0031722 | 0.7618805 | 0.0328097 |
| 7123 | GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 2B COMPLEX | 5 | 0.0032020 | -0.7611349 | 0.0329784 |
| 7695 | GOCC THO COMPLEX | 6 | 0.0012694 | -0.7596811 | 0.0169632 |
| 7275 | GOCC LSM1 7 PAT1 COMPLEX | 5 | 0.0032631 | -0.7596254 | 0.0333088 |
| 7478 | GOCC PICLN SM PROTEIN COMPLEX | 6 | 0.0013264 | -0.7567105 | 0.0174760 |
| 3284 | GOBP OBSERVATIONAL LEARNING | 6 | 0.0013491 | 0.7555586 | 0.0176581 |
| 7462 | GOCC PHAGOCYTIC VESICLE LUMEN | 5 | 0.0035437 | 0.7530054 | 0.0353274 |
| 9239 | GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | 7 | 0.0006140 | -0.7475316 | 0.0097798 |
| 7581 | GOCC RIBOSOMAL SUBUNIT | 182 | 0.0000000 | -0.7461265 | 0.0000000 |
| 7264 | GOCC LARGE RIBOSOMAL SUBUNIT | 110 | 0.0000000 | -0.7449246 | 0.0000000 |
| 8287 | GOMF GLUTAMATE GATED CALCIUM ION CHANNEL ACTIVITY | 5 | 0.0039916 | 0.7433664 | 0.0384052 |
| 7052 | GOCC CYTOSOLIC SMALL RIBOSOMAL SUBUNIT | 43 | 0.0000000 | -0.7411271 | 0.0000000 |
| 6879 | GOCC BASAL CORTEX | 5 | 0.0041606 | 0.7399836 | 0.0398676 |
| 1734 | GOBP INNER CELL MASS CELL DIFFERENTIATION | 6 | 0.0017004 | 0.7397202 | 0.0208356 |
| 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 | -0.7362781 | 0.0000000 |
| 7133 | GOCC EXTERNAL SIDE OF APICAL PLASMA MEMBRANE | 5 | 0.0044439 | 0.7345822 | 0.0418069 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/crp_eos_b_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/34
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac31619860a.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- crp_pod1_a_adj
myname <- "crp_pod1_a_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0003721 | 0.9189947 | 0.0053427 |
| 1263 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0000814 | 0.8598593 | 0.0015693 |
| 1796 | GOBP INTRACELLULAR GLUTAMATE HOMEOSTASIS | 5 | 0.0009512 | -0.8532756 | 0.0111030 |
| 2664 | GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 6 | 0.0005017 | 0.8202570 | 0.0066792 |
| 181 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0015610 | -0.8167545 | 0.0164068 |
| 8428 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0015610 | -0.8167545 | 0.0164068 |
| 7220 | GOCC MESSENGER RIBONUCLEOPROTEIN COMPLEX | 6 | 0.0006063 | 0.8082239 | 0.0077802 |
| 5674 | GOBP REGULATION OF TERMINATION OF DNA TEMPLATED TRANSCRIPTION | 5 | 0.0024114 | 0.7834902 | 0.0224496 |
| 7092 | GOCC F ACTIN CAPPING PROTEIN COMPLEX | 7 | 0.0003853 | 0.7747206 | 0.0054738 |
| 4970 | GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 6 | 0.0012376 | 0.7613938 | 0.0137378 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0002419 | 0.7493528 | 0.0037513 |
| 9075 | GOMF SPHINGOSINE 1 PHOSPHATE RECEPTOR ACTIVITY | 7 | 0.0005970 | -0.7491965 | 0.0077042 |
| 7759 | GOMF ADENINE TRANSMEMBRANE TRANSPORTER ACTIVITY | 5 | 0.0043364 | -0.7365964 | 0.0344059 |
| 7149 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 7 | 0.0007923 | -0.7322925 | 0.0096348 |
| 1115 | GOBP EMBRYONIC DIGESTIVE TRACT MORPHOGENESIS | 6 | 0.0019414 | 0.7305188 | 0.0193870 |
| 1748 | GOBP INTERKINETIC NUCLEAR MIGRATION | 5 | 0.0046901 | 0.7301393 | 0.0361022 |
| 1791 | GOBP INTRACELLULAR AMINO ACID HOMEOSTASIS | 7 | 0.0008827 | -0.7257433 | 0.0104550 |
| 174 | GOBP ANTEROGRADE DENDRITIC TRANSPORT | 8 | 0.0003964 | 0.7231819 | 0.0055965 |
| 8284 | GOMF HISTONE H2A UBIQUITIN LIGASE ACTIVITY | 6 | 0.0022642 | 0.7197094 | 0.0215320 |
| 2092 | GOBP MAST CELL CYTOKINE PRODUCTION | 6 | 0.0022728 | 0.7194427 | 0.0215767 |
| 7533 | GOCC SARCOPLASMIC RETICULUM LUMEN | 5 | 0.0059212 | 0.7106551 | 0.0429458 |
| 7261 | GOCC MITOTIC COHESIN COMPLEX | 7 | 0.0011754 | 0.7081400 | 0.0131893 |
| 6952 | GOCC CRD MEDIATED MRNA STABILITY COMPLEX | 5 | 0.0066451 | 0.7008471 | 0.0465608 |
| 762 | GOBP CHOLINE TRANSPORT | 5 | 0.0067869 | 0.6990399 | 0.0472689 |
| 2465 | GOBP NEGATIVE REGULATION OF ADENYLATE CYCLASE ACTIVATING ADRENERGIC RECEPTOR SIGNALING PATHWAY | 5 | 0.0068482 | 0.6982681 | 0.0474473 |
| 7414 | GOCC PLATELET DENSE GRANULE MEMBRANE | 6 | 0.0031619 | 0.6957531 | 0.0271258 |
| 6784 | GOCC ARP2 3 PROTEIN COMPLEX | 9 | 0.0003092 | 0.6943346 | 0.0046190 |
| 3539 | GOBP POSITIVE REGULATION OF AGGREPHAGY | 5 | 0.0072223 | 0.6936935 | 0.0491952 |
| 353 | GOBP BRANCHING INVOLVED IN LABYRINTHINE LAYER MORPHOGENESIS | 10 | 0.0001480 | 0.6928494 | 0.0025415 |
| 65 | GOBP ADENINE TRANSPORT | 6 | 0.0039468 | -0.6794528 | 0.0320129 |
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/Rtmpadl22y/crp_pod1_a_adj_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/34
## 2/34 [checklibraries]
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## 29/34 [detailed_geneset_reports1d]## 30/34
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac3788ba637.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.9148075 | 0.0011165 |
| 3151 | GOBP NITRIC OXIDE TRANSPORT | 5 | 0.0006876 | 0.8764872 | 0.0129806 |
| 181 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0007754 | -0.8679593 | 0.0141124 |
| 8428 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0007754 | -0.8679593 | 0.0141124 |
| 7139 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0000025 | 0.8589747 | 0.0001555 |
| 7136 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0000086 | 0.8563673 | 0.0004251 |
| 8261 | GOMF HAPTOGLOBIN BINDING | 8 | 0.0000303 | 0.8515062 | 0.0012081 |
| 4100 | GOBP POSITIVE REGULATION OF PROTEIN LOCALIZATION TO SYNAPSE | 5 | 0.0010413 | 0.8467056 | 0.0172462 |
| 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 | 0.0281130 |
| 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 | 0.0003323 | 0.7326194 | 0.0075666 |
| 3479 | GOBP PLASMA CELL DIFFERENTIATION | 8 | 0.0003337 | 0.7323841 | 0.0075815 |
| 7111 | GOCC GLYCOPROTEIN IB IX V COMPLEX | 5 | 0.0046338 | 0.7311370 | 0.0486466 |
| 6832 | GOCC BRCA1 C COMPLEX | 6 | 0.0020657 | -0.7261731 | 0.0281329 |
| 4074 | GOBP POSITIVE REGULATION OF PROTEIN CATABOLIC PROCESS IN THE VACUOLE | 6 | 0.0028473 | 0.7033464 | 0.0346060 |
| 1841 | GOBP ISG15 PROTEIN CONJUGATION | 6 | 0.0029352 | -0.7011500 | 0.0352340 |
| 2710 | GOBP NEGATIVE REGULATION OF INFLAMMATORY RESPONSE TO WOUNDING | 7 | 0.0017243 | 0.6839741 | 0.0247990 |
| 3334 | GOBP OXYGEN TRANSPORT | 10 | 0.0001883 | 0.6818717 | 0.0049409 |
| 1403 | GOBP FORMATION OF TRANSLATION PREINITIATION COMPLEX | 7 | 0.0021191 | -0.6706607 | 0.0284932 |
| 6733 | GOBP WYBUTOSINE METABOLIC PROCESS | 6 | 0.0044704 | -0.6701495 | 0.0477277 |
| 8721 | GOMF OXYGEN CARRIER ACTIVITY | 9 | 0.0005134 | 0.6685914 | 0.0103722 |
| 5120 | GOBP REGULATION OF INFLAMMATORY RESPONSE TO WOUNDING | 9 | 0.0005360 | 0.6663633 | 0.0106871 |
| 1098 | GOBP ECTODERMAL CELL DIFFERENTIATION | 6 | 0.0048122 | 0.6645958 | 0.0497890 |
| 3519 | GOBP POLY N ACETYLLACTOSAMINE METABOLIC PROCESS | 7 | 0.0025427 | 0.6587055 | 0.0322732 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/crp_pod1_b_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac37af3f2c8.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- avb_crplo_t0_adj
myname <- "avb_crplo_t0_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21935## Note: no. genes in output = 21870## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | -0.8836995 | 0.0002815 |
| 1953 | GOBP LIPOXIN METABOLIC PROCESS | 5 | 0.0006376 | -0.8818020 | 0.0161118 |
| 8034 | GOMF COMPLEMENT COMPONENT C3B BINDING | 5 | 0.0013422 | -0.8280357 | 0.0283902 |
| 8385 | GOMF ICOSANOID BINDING | 7 | 0.0002328 | -0.8031900 | 0.0075579 |
| 182 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0024849 | -0.7811480 | 0.0442507 |
| 8479 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0024849 | -0.7811480 | 0.0442507 |
| 4168 | GOBP POSITIVE REGULATION OF RIG I SIGNALING PATHWAY | 8 | 0.0001394 | 0.7776164 | 0.0050511 |
| 8142 | GOMF DNA RNA HYBRID BINDING | 5 | 0.0027192 | 0.7740864 | 0.0469904 |
| 1270 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0003902 | 0.7739952 | 0.0111060 |
| 9176 | GOMF SUPEROXIDE GENERATING NADPH OXIDASE ACTIVATOR ACTIVITY | 10 | 0.0000227 | -0.7735041 | 0.0011608 |
| 9304 | GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 5 | 0.0027734 | 0.7725314 | 0.0476632 |
| 7855 | GOMF ANKYRIN REPEAT BINDING | 6 | 0.0011062 | 0.7689200 | 0.0245346 |
| 5581 | GOBP REGULATION OF RESPIRATORY BURST INVOLVED IN INFLAMMATORY RESPONSE | 6 | 0.0012483 | -0.7608092 | 0.0268686 |
| 8653 | GOMF NERVE GROWTH FACTOR BINDING | 6 | 0.0017332 | -0.7383980 | 0.0344768 |
| 6410 | GOBP SYNAPSE PRUNING | 9 | 0.0001340 | -0.7350228 | 0.0049335 |
| 4533 | GOBP PROTEIN REPAIR | 7 | 0.0008966 | -0.7247927 | 0.0211521 |
| 1725 | GOBP INNATE IMMUNE RESPONSE IN MUCOSA | 17 | 0.0000003 | -0.7186226 | 0.0000261 |
| 8868 | GOMF PHOSPHOLIPASE INHIBITOR ACTIVITY | 7 | 0.0010159 | -0.7171477 | 0.0232225 |
| 8565 | GOMF MHC CLASS I PROTEIN COMPLEX BINDING | 7 | 0.0011882 | 0.7074640 | 0.0260767 |
| 1629 | GOBP HEPOXILIN METABOLIC PROCESS | 7 | 0.0012211 | -0.7057651 | 0.0265979 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0013188 | -0.7009560 | 0.0280207 |
| 7744 | GOMF 1 PHOSPHATIDYLINOSITOL 4 PHOSPHATE 3 KINASE ACTIVITY | 7 | 0.0013420 | 0.6998582 | 0.0283902 |
| 5892 | GOBP RESPONSE TO CORTICOSTERONE | 11 | 0.0000650 | -0.6953450 | 0.0026881 |
| 8751 | GOMF OXIDOREDUCTASE ACTIVITY ACTING ON DIPHENOLS AND RELATED SUBSTANCES AS DONORS | 9 | 0.0003283 | -0.6913428 | 0.0098573 |
| 5848 | GOBP RESPIRATORY BURST INVOLVED IN INFLAMMATORY RESPONSE | 8 | 0.0011053 | -0.6659844 | 0.0245346 |
| 1771 | GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 7 | 0.0025260 | 0.6591371 | 0.0447272 |
| 5945 | GOBP RESPONSE TO INTERFERON ALPHA | 18 | 0.0000016 | 0.6532735 | 0.0001126 |
| 2622 | GOBP NEGATIVE REGULATION OF DIGESTIVE SYSTEM PROCESS | 10 | 0.0004743 | 0.6381702 | 0.0129266 |
| 7333 | GOCC NADPH OXIDASE COMPLEX | 14 | 0.0000420 | -0.6321899 | 0.0019052 |
| 8664 | GOMF NEUROTROPHIN BINDING | 8 | 0.0021740 | -0.6258005 | 0.0400874 |
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/Rtmpadl22y/avb_crplo_t0_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac32d3c0e41.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.8563032 | 0.0004041 |
| 2070 | GOBP MAINTENANCE OF PROTEIN LOCATION IN MITOCHONDRION | 5 | 0.0012071 | 0.8358838 | 0.0099429 |
| 8204 | GOMF FATTY ACYL COA SYNTHASE ACTIVITY | 5 | 0.0012225 | -0.8349508 | 0.0100430 |
| 3494 | GOBP PLANAR CELL POLARITY PATHWAY INVOLVED IN NEURAL TUBE CLOSURE | 6 | 0.0004268 | 0.8304061 | 0.0042269 |
| 7170 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0000163 | 0.8296916 | 0.0002589 |
| 8306 | GOMF HAPTOGLOBIN BINDING | 8 | 0.0000514 | 0.8265827 | 0.0006923 |
| 7173 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0000070 | 0.8204941 | 0.0001222 |
| 7186 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 11 | 0.0000027 | 0.8168177 | 0.0000520 |
| 8228 | GOMF GABA A RECEPTOR ACTIVITY | 5 | 0.0019108 | -0.8014361 | 0.0144005 |
| 8310 | GOMF HEMOGLOBIN BINDING | 7 | 0.0002893 | 0.7910364 | 0.0030080 |
| 7665 | GOCC TORC1 COMPLEX | 6 | 0.0013649 | 0.7547719 | 0.0109529 |
| 8406 | GOMF INOSITOL POLYPHOSPHATE 5 PHOSPHATASE ACTIVITY | 6 | 0.0013993 | 0.7530796 | 0.0111621 |
| 9288 | GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | 7 | 0.0005702 | 0.7519096 | 0.0053447 |
| 6926 | GOCC CHROMOSOME PASSENGER COMPLEX | 6 | 0.0014817 | 0.7491767 | 0.0117098 |
| 2912 | GOBP NEGATIVE REGULATION OF PROTEIN LOCALIZATION TO CHROMATIN | 6 | 0.0014860 | 0.7489785 | 0.0117240 |
| 6332 | GOBP SPINDLE ELONGATION | 13 | 0.0000033 | 0.7449013 | 0.0000621 |
| 7189 | GOCC IMMUNOGLOBULIN COMPLEX | 112 | 0.0000000 | 0.7437683 | 0.0000000 |
| 8429 | GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | 6 | 0.0016460 | 0.7419655 | 0.0127299 |
| 2306 | GOBP MITOTIC SPINDLE ELONGATION | 11 | 0.0000208 | 0.7410095 | 0.0003206 |
| 6334 | GOBP SPINDLE MIDZONE ASSEMBLY | 13 | 0.0000042 | 0.7367504 | 0.0000770 |
| 9318 | GOMF UNMETHYLATED CPG BINDING | 10 | 0.0000648 | 0.7294145 | 0.0008396 |
| 1989 | GOBP LYMPHOCYTE AGGREGATION | 5 | 0.0054586 | 0.7175029 | 0.0334640 |
| 7162 | GOCC GROWTH CONE MEMBRANE | 6 | 0.0026345 | 0.7089279 | 0.0188444 |
| 1851 | GOBP ISOLEUCINE TRANSPORT | 5 | 0.0062475 | 0.7061056 | 0.0372025 |
| 7185 | GOCC IGE IMMUNOGLOBULIN COMPLEX | 5 | 0.0067690 | 0.6992637 | 0.0394536 |
| 1274 | GOBP ESTABLISHMENT OF PLANAR POLARITY INVOLVED IN NEURAL TUBE CLOSURE | 7 | 0.0014531 | 0.6948530 | 0.0115224 |
| 6956 | GOCC CMG COMPLEX | 11 | 0.0000709 | 0.6917267 | 0.0009022 |
| 2787 | GOBP NEGATIVE REGULATION OF MEIOTIC CELL CYCLE PHASE TRANSITION | 5 | 0.0074829 | 0.6906289 | 0.0421938 |
| 4978 | GOBP REGULATION OF DNA TEMPLATED DNA REPLICATION INITIATION | 14 | 0.0000083 | 0.6877876 | 0.0001418 |
| 4517 | GOBP PROTEIN O LINKED FUCOSYLATION | 5 | 0.0080382 | 0.6844089 | 0.0443105 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/avb_crphi_t0_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac37c48278f.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- avb_crplo_eos_adj
myname <- "avb_crplo_eos_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 22067## Note: no. genes in output = 21999## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | -0.8832962 | 0.0085091 |
| 411 | GOBP CANNABINOID SIGNALING PATHWAY | 7 | 0.0000655 | -0.8711999 | 0.0039678 |
| 183 | GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | 5 | 0.0007608 | -0.8693098 | 0.0246845 |
| 8512 | GOMF LIPID ANTIGEN BINDING | 5 | 0.0007608 | -0.8693098 | 0.0246845 |
| 5275 | GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | 5 | 0.0011823 | -0.8374102 | 0.0334078 |
| 6996 | GOCC COLLAGEN TYPE IV TRIMER | 5 | 0.0014127 | -0.8242248 | 0.0380832 |
| 7386 | GOCC NLRP1 INFLAMMASOME COMPLEX | 5 | 0.0017220 | 0.8093480 | 0.0438902 |
| 8123 | GOMF C PALMITOYLTRANSFERASE ACTIVITY | 5 | 0.0017898 | -0.8064199 | 0.0452124 |
| 8696 | GOMF NEUROTROPHIN BINDING | 9 | 0.0000385 | -0.7922288 | 0.0025991 |
| 4866 | GOBP REGULATION OF CELLULAR PH REDUCTION | 6 | 0.0008596 | -0.7856136 | 0.0265998 |
| 6883 | GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 6 | 0.0008620 | -0.7854317 | 0.0265998 |
| 821 | GOBP COLLAGEN ACTIVATED TYROSINE KINASE RECEPTOR SIGNALING PATHWAY | 10 | 0.0000212 | -0.7764246 | 0.0016678 |
| 6308 | GOBP SNORNA LOCALIZATION | 6 | 0.0011348 | 0.7672138 | 0.0326146 |
| 7219 | GOCC IGA IMMUNOGLOBULIN COMPLEX | 9 | 0.0000859 | -0.7558688 | 0.0048847 |
| 1859 | GOBP ISOLEUCINE METABOLIC PROCESS | 7 | 0.0007079 | 0.7390610 | 0.0238012 |
| 100 | GOBP ALKANESULFONATE TRANSMEMBRANE TRANSPORT | 6 | 0.0019253 | -0.7310963 | 0.0475700 |
| 7964 | GOMF C3HC4 TYPE RING FINGER DOMAIN BINDING | 6 | 0.0019320 | 0.7308538 | 0.0475700 |
| 190 | GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | 7 | 0.0010839 | -0.7131554 | 0.0316776 |
| 820 | GOBP COLLAGEN ACTIVATED SIGNALING PATHWAY | 14 | 0.0000053 | -0.7022710 | 0.0005514 |
| 7247 | GOCC INTRACILIARY TRANSPORT PARTICLE A | 8 | 0.0006004 | 0.7005138 | 0.0214968 |
| 1340 | GOBP FACIAL NERVE MORPHOGENESIS | 7 | 0.0019603 | 0.6757132 | 0.0481413 |
| 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 | 0.0150977 |
| 7298 | GOCC MHC CLASS II PROTEIN COMPLEX | 15 | 0.0000149 | 0.6457242 | 0.0012667 |
| 8559 | GOMF MANGANESE ION TRANSMEMBRANE TRANSPORTER ACTIVITY | 8 | 0.0015731 | -0.6452867 | 0.0411063 |
| 3799 | GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | 10 | 0.0004245 | 0.6435490 | 0.0163209 |
| 7224 | GOCC IGM IMMUNOGLOBULIN COMPLEX | 9 | 0.0008861 | -0.6398666 | 0.0271178 |
| 8596 | GOMF MHC CLASS II RECEPTOR ACTIVITY | 9 | 0.0008874 | 0.6397858 | 0.0271178 |
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/Rtmpadl22y/avb_crplo_eos_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac359474a94.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.0183751 |
| 6362 | GOBP SPINDLE ELONGATION | 13 | 0.0000409 | 0.6570125 | 0.0123745 |
| 91 | GOBP ALANINE TRANSPORT | 13 | 0.0001156 | -0.6174419 | 0.0226947 |
| 3438 | GOBP PERK MEDIATED UNFOLDED PROTEIN RESPONSE | 19 | 0.0001295 | -0.5071213 | 0.0242928 |
| 7246 | GOCC INTRACILIARY TRANSPORT PARTICLE | 22 | 0.0001045 | 0.4777764 | 0.0213045 |
| 7735 | GOCC T CELL RECEPTOR COMPLEX | 121 | 0.0000000 | 0.4520175 | 0.0000000 |
| 7226 | GOCC IMMUNOGLOBULIN COMPLEX | 109 | 0.0000000 | 0.4228993 | 0.0000000 |
| 8751 | GOMF OLFACTORY RECEPTOR ACTIVITY | 54 | 0.0000016 | -0.3777001 | 0.0009804 |
| 1068 | GOBP DNA REPLICATION INITIATION | 35 | 0.0002647 | 0.3562167 | 0.0423780 |
| 1834 | GOBP INTRACILIARY TRANSPORT | 43 | 0.0000674 | 0.3511992 | 0.0183751 |
| 295 | GOBP BASE EXCISION REPAIR | 43 | 0.0000995 | 0.3429608 | 0.0207324 |
| 7893 | GOMF ANTIGEN BINDING | 151 | 0.0000000 | 0.3426110 | 0.0000000 |
| 6227 | GOBP SENSORY PERCEPTION OF SMELL | 71 | 0.0000031 | -0.3200667 | 0.0018133 |
| 107 | GOBP ALTERNATIVE MRNA SPLICING VIA SPLICEOSOME | 67 | 0.0000127 | -0.3082595 | 0.0059210 |
| 5357 | GOBP REGULATION OF MRNA SPLICING VIA SPLICEOSOME | 98 | 0.0000139 | -0.2539703 | 0.0059210 |
| 5914 | GOBP RESPONSE TO CHEMOKINE | 67 | 0.0003314 | -0.2535449 | 0.0485702 |
| 7571 | GOCC REPLICATION FORK | 74 | 0.0002660 | 0.2451133 | 0.0423780 |
| 6942 | GOCC CENTRIOLE | 152 | 0.0000009 | 0.2307447 | 0.0006060 |
| 6223 | GOBP SENSORY PERCEPTION OF CHEMICAL STIMULUS | 103 | 0.0000873 | -0.2236965 | 0.0204697 |
| 7484 | GOCC PLASMA MEMBRANE SIGNALING RECEPTOR COMPLEX | 248 | 0.0000000 | 0.2216895 | 0.0000015 |
| 625 | GOBP CELLULAR RESPONSE TO TOPOLOGICALLY INCORRECT PROTEIN | 97 | 0.0001899 | -0.2192390 | 0.0336156 |
| 983 | GOBP DETECTION OF STIMULUS INVOLVED IN SENSORY PERCEPTION | 124 | 0.0000264 | -0.2184568 | 0.0088579 |
| 5332 | GOBP REGULATION OF MITOTIC NUCLEAR DIVISION | 107 | 0.0001741 | 0.2100123 | 0.0314084 |
| 8956 | GOMF PROTEASE BINDING | 116 | 0.0000980 | -0.2093461 | 0.0207324 |
| 5356 | GOBP REGULATION OF MRNA PROCESSING | 120 | 0.0000911 | -0.2067835 | 0.0207324 |
| 4699 | GOBP RECEPTOR INTERNALIZATION | 104 | 0.0003254 | -0.2039472 | 0.0484478 |
| 1075 | GOBP DNA TEMPLATED DNA REPLICATION | 160 | 0.0000152 | 0.1981163 | 0.0059520 |
| 6074 | GOBP RESPONSE TO TOPOLOGICALLY INCORRECT PROTEIN | 140 | 0.0000959 | -0.1909191 | 0.0207324 |
vec <- mtop$s.dist
names(vec) <- mtop$set
vec <- sort(vec)
par( mar = c(5.1, 25.1, 4.1, 2.1) )
barplot(vec,horiz=TRUE,las=1,cex.names=0.7,xlab="ES",main=myname)
par( mar = c(5.1, 4.1, 4.1, 2.1) )
mitch_report(res=mres,outfile=paste(myname,"_mitchreport.html",sep=""),overwrite=TRUE)## Note: overwriting existing report## Dataset saved as " /tmp/Rtmpadl22y/avb_crphi_eos_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpadl22y/rmarkdown-str3ffac376c16540.html##
## Output created: /tmp/Rtmpadl22y/mitch_report.html## [1] TRUEde <- avb_crplo_pod1_adj
myname <- "avb_crplo_pod1_adj"
m <- mitch_import(x=de, DEtype="deseq2", geneTable=gt )## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21313## Note: no. genes in output = 21253## Note: estimated proportion of input genes in output = 0.997mres <- mitch_calc(x=m,genesets=go,minsetsize=5,cores=16,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.mtop <- head(subset (mres$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 | 0.0002541 | 0.8622551 | 0.0287918 |
| 1263 | GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 7 | 0.0001084 | 0.8447573 | 0.0162440 |
| 1764 | GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 7 | 0.0002649 | 0.7959818 | 0.0291240 |
| 4393 | GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 11 | 0.0000525 | 0.7040683 | 0.0088744 |
| 8588 | GOMF NADPLUS NUCLEOTIDASE CYCLIC ADP RIBOSE GENERATING | 13 | 0.0001493 | 0.6073664 | 0.0203968 |
| 4007 | GOBP POSITIVE REGULATION OF NITRIC OXIDE SYNTHASE BIOSYNTHETIC PROCESS | 14 | 0.0001474 | 0.5857688 | 0.0203968 |
| 5916 | GOBP RESPONSE TO INTERFERON ALPHA | 18 | 0.0000735 | 0.5396803 | 0.0119814 |
| 4107 | GOBP POSITIVE REGULATION OF PROTEIN POLYUBIQUITINATION | 16 | 0.0002008 | 0.5367931 | 0.0245488 |
| 2292 | GOBP MITOTIC SISTER CHROMATID COHESION | 31 | 0.0000025 | 0.4882973 | 0.0011150 |
| 1041 | GOBP DNA DOUBLE STRAND BREAK PROCESSING | 20 | 0.0002484 | 0.4731880 | 0.0284888 |
| 7259 | GOCC MITOCHONDRIA ASSOCIATED ENDOPLASMIC RETICULUM MEMBRANE CONTACT SITE | 20 | 0.0003811 | 0.4588424 | 0.0384890 |
| 5516 | GOBP REGULATION OF PROTEIN POLYUBIQUITINATION | 24 | 0.0005188 | 0.4092397 | 0.0471931 |
| 8196 | GOMF GDP BINDING | 64 | 0.0000004 | 0.3667690 | 0.0004557 |
| 1272 | GOBP ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 42 | 0.0000610 | 0.3574403 | 0.0101246 |
| 3050 | GOBP NEGATIVE REGULATION OF VIRAL GENOME REPLICATION | 50 | 0.0000821 | 0.3218903 | 0.0127134 |
| 257 | GOBP ATTACHMENT OF SPINDLE MICROTUBULES TO KINETOCHORE | 51 | 0.0001346 | 0.3089923 | 0.0192411 |
| 8108 | GOMF DOUBLE STRANDED RNA BINDING | 70 | 0.0000090 | 0.3067608 | 0.0030992 |
| 5764 | GOBP REGULATION OF VIRAL GENOME REPLICATION | 78 | 0.0000101 | 0.2891545 | 0.0032236 |
| 816 | GOBP COLLAGEN METABOLIC PROCESS | 73 | 0.0002288 | -0.2494056 | 0.0270762 |
| 4452 | GOBP PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 71 | 0.0004877 | 0.2393356 | 0.0453090 |
| 4383 | GOBP PROTEIN DEUBIQUITINATION | 82 | 0.0004213 | 0.2252483 | 0.0405341 |
| 4485 | GOBP PROTEIN MODIFICATION BY SMALL PROTEIN REMOVAL | 102 | 0.0000866 | 0.2249131 | 0.0131880 |
| 1164 | GOBP ENDOPLASMIC RETICULUM TO GOLGI VESICLE MEDIATED TRANSPORT | 132 | 0.0000083 | 0.2246034 | 0.0029780 |
| 7558 | GOCC SITE OF DOUBLE STRAND BREAK | 94 | 0.0002368 | 0.2193745 | 0.0275005 |
| 6698 | GOBP VIRAL GENOME REPLICATION | 117 | 0.0000812 | 0.2108939 | 0.0127134 |
| 6890 | GOCC CHROMOSOME CENTROMERIC REGION | 242 | 0.0000000 | 0.2093052 | 0.0000630 |
| 4420 | GOBP PROTEIN K48 LINKED UBIQUITINATION | 97 | 0.0004116 | 0.2075383 | 0.0402502 |
| 5765 | GOBP REGULATION OF VIRAL PROCESS | 143 | 0.0000267 | 0.2034220 | 0.0053976 |
| 9243 | GOMF UBIQUITIN LIKE PROTEIN PEPTIDASE ACTIVITY | 106 | 0.0003375 | 0.2015041 | 0.0349459 |
| 7557 | GOCC SITE OF DNA DAMAGE | 125 | 0.0001685 | 0.1948300 | 0.0220477 |
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/Rtmpadl22y/avb_crplo_pod1_adj_mitchreport.rds ".##
##
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## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac37698f669.html##
## Output created: /tmp/Rtmpadl22y/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 | 0.9867269 | 0.0009993 |
| 7150 | GOCC IGG IMMUNOGLOBULIN COMPLEX | 10 | 0.0000001 | 0.9748246 | 0.0000296 |
| 8860 | GOMF PRIMARY AMINE OXIDASE ACTIVITY | 7 | 0.0000689 | -0.8685198 | 0.0066722 |
| 8265 | GOMF HEMOGLOBIN BINDING | 7 | 0.0000918 | 0.8535523 | 0.0081254 |
| 2439 | GOBP NAIL DEVELOPMENT | 5 | 0.0010475 | 0.8462726 | 0.0467921 |
| 7151 | GOCC IGM IMMUNOGLOBULIN COMPLEX | 8 | 0.0000660 | 0.8145799 | 0.0064518 |
| 6764 | GOCC ALPHA BETA T CELL RECEPTOR COMPLEX | 10 | 0.0000086 | 0.8125783 | 0.0013497 |
| 7153 | GOCC IMMUNOGLOBULIN COMPLEX | 106 | 0.0000000 | 0.8017088 | 0.0000000 |
| 7154 | GOCC IMMUNOGLOBULIN COMPLEX CIRCULATING | 11 | 0.0000705 | 0.6919568 | 0.0067182 |
| 1468 | GOBP GLOMERULAR MESANGIAL CELL PROLIFERATION | 8 | 0.0007587 | 0.6874559 | 0.0376575 |
| 6923 | GOCC CMG COMPLEX | 11 | 0.0001053 | 0.6751889 | 0.0088370 |
| 4342 | GOBP PROLINE METABOLIC PROCESS | 8 | 0.0010154 | 0.6708755 | 0.0460222 |
| 3535 | GOBP POSITIVE REGULATION OF ACUTE INFLAMMATORY RESPONSE TO ANTIGENIC STIMULUS | 8 | 0.0011746 | 0.6624618 | 0.0489365 |
| 7136 | GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 9 | 0.0007160 | 0.6512166 | 0.0361564 |
| 7139 | GOCC HEMOGLOBIN COMPLEX | 10 | 0.0006189 | 0.6250812 | 0.0326737 |
| 7004 | GOCC DNA REPLICATION PREINITIATION COMPLEX | 12 | 0.0001865 | 0.6228913 | 0.0141243 |
| 3334 | GOBP OXYGEN TRANSPORT | 10 | 0.0008127 | 0.6114391 | 0.0387201 |
| 4675 | GOBP REGULATION OF ACUTE INFLAMMATORY RESPONSE TO ANTIGENIC STIMULUS | 14 | 0.0002948 | 0.5586758 | 0.0192774 |
| 7362 | GOCC OUTER KINETOCHORE | 18 | 0.0000517 | 0.5509929 | 0.0054590 |
| 8514 | GOMF MHC CLASS I RECEPTOR ACTIVITY | 12 | 0.0011131 | 0.5434929 | 0.0478706 |
| 692 | GOBP CELL PROLIFERATION INVOLVED IN KIDNEY DEVELOPMENT | 14 | 0.0006292 | 0.5276479 | 0.0330292 |
| 8715 | GOMF OXIDOREDUCTASE ACTIVITY ACTING ON THE CH NH2 GROUP OF DONORS OXYGEN AS ACCEPTOR | 14 | 0.0007563 | -0.5198725 | 0.0376575 |
| 2281 | GOBP MITOTIC DNA REPLICATION | 17 | 0.0003531 | 0.5004598 | 0.0218683 |
| 2986 | GOBP NEGATIVE REGULATION OF SYSTEMIC ARTERIAL BLOOD PRESSURE | 16 | 0.0010971 | -0.4713177 | 0.0476301 |
| 6444 | GOBP THYMIC T CELL SELECTION | 21 | 0.0002678 | 0.4593650 | 0.0177694 |
| 2128 | GOBP MEIOTIC SPINDLE ORGANIZATION | 17 | 0.0011140 | 0.4566496 | 0.0478706 |
| 1069 | GOBP DNA UNWINDING INVOLVED IN DNA REPLICATION | 21 | 0.0003134 | 0.4542425 | 0.0202185 |
| 7659 | GOCC T CELL RECEPTOR COMPLEX | 119 | 0.0000000 | 0.4535668 | 0.0000000 |
| 7815 | GOMF ANTIGEN BINDING | 149 | 0.0000000 | 0.4460766 | 0.0000000 |
| 8345 | GOMF IMMUNOGLOBULIN RECEPTOR BINDING | 19 | 0.0011867 | 0.4295841 | 0.0491475 |
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/Rtmpadl22y/avb_crphi_pod1_adj_mitchreport.rds ".##
##
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## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac36c9df929.html##
## Output created: /tmp/Rtmpadl22y/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 | -0.1513768 | -0.8247586 | -0.7277786 | -0.8153992 | -0.8672374 | -0.7827555 | 0.3877776 | -0.8720883 | -0.3432824 | -0.5662339 | -0.5058734 |
| GOMF LIPID ANTIGEN BINDING | -0.9772863 | -0.1513768 | -0.8247586 | -0.7277786 | -0.8153992 | -0.8672374 | -0.7827555 | 0.3877776 | -0.8720883 | -0.3432824 | -0.5662339 | -0.5058734 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.8176185 | 0.3074231 | -0.8559402 | 0.3783999 | -0.7304162 | 0.3926822 | -0.5288330 | 0.9654017 | -0.7973569 | 0.6854765 | -0.4239511 | 0.9866146 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.7041100 | 0.2422795 | -0.7386072 | 0.3795357 | -0.5459328 | 0.4052707 | -0.0886785 | 0.8876891 | -0.6149462 | 0.7413852 | -0.2219579 | 0.9746456 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1435963 | 0.6828268 | -0.1372236 | 0.7577400 | -0.1387644 | 0.8112332 | -0.7357303 | 0.6567651 | -0.5790745 | 0.1831074 | -0.8472250 | 0.5190755 |
| GOMF INTERLEUKIN 1 RECEPTOR ACTIVITY | -0.2651733 | -0.4091026 | 0.2474057 | 0.7023636 | 0.6807343 | 0.3248870 | -0.6098540 | -0.1843439 | -0.9779902 | -0.8812765 | 0.4341561 | -0.3078803 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.2564498 | -0.8110277 | 0.5939392 | 0.4723153 | 0.8614031 | -0.4579242 | 0.7744590 | -0.0156752 | -0.1150127 | -0.0781043 | 0.8442127 | -0.0886088 |
| GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 0.4689685 | -0.9036667 | 0.4065154 | 0.1409711 | 0.2104818 | -0.8263376 | 0.7731298 | -0.4399011 | -0.0885623 | 0.4333000 | 0.7371380 | -0.1842298 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8968754 | 0.1635326 | -0.8200789 | -0.9202549 | -0.3959195 | -0.4307700 | -0.2687687 | 0.3940362 | 0.7311457 | -0.1680411 | -0.1533742 | 0.0362296 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.7476578 | 0.2310078 | -0.3077282 | 0.5061587 | 0.4883721 | 0.4842821 | -0.6555667 | 0.2948305 | -0.6791363 | -0.8289057 | -0.0245874 | 0.0284111 |
| GOMF HEMOGLOBIN BINDING | 0.1905691 | 0.4423917 | 0.0973875 | 0.5064787 | 0.4205402 | 0.9159504 | 0.0709563 | 0.7876270 | -0.2173943 | -0.0914082 | 0.3416681 | 0.8529777 |
| GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | -0.2339373 | -0.3676131 | 0.3663005 | 0.1124744 | 0.5426642 | -0.3071004 | -0.3605555 | -0.2102345 | -0.8408332 | -0.8155705 | 0.7958434 | -0.3454130 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8528559 | 0.0632235 | -0.7918105 | -0.8148095 | 0.1666144 | -0.3834784 | -0.4637561 | 0.6158843 | 0.4196034 | -0.1887002 | -0.0374281 | 0.0142198 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.1280003 | -0.8113605 | 0.4112052 | 0.2617870 | 0.7632772 | -0.3513586 | 0.4078601 | -0.3011510 | -0.3882812 | -0.3939725 | 0.8618536 | 0.2531945 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.8338169 | -0.1294717 | -0.5952030 | -0.3631663 | -0.4672465 | -0.6066452 | -0.4781043 | 0.3901818 | -0.7187158 | -0.2820656 | -0.3736980 | -0.2184542 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8170180 | 0.1512484 | -0.7174085 | -0.8739660 | -0.3355082 | -0.3955580 | -0.3507498 | 0.3809086 | 0.6510816 | 0.0098225 | -0.0298929 | 0.0221548 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7866743 | -0.5168307 | -0.7390213 | -0.2599420 | 0.5222333 | -0.2271651 | -0.1640462 | 0.5086698 | 0.0176059 | -0.5793408 | 0.5911923 | 0.2668664 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.8342653 | 0.3530559 | -0.7173705 | -0.4390352 | 0.1851877 | -0.2089553 | -0.7035366 | 0.7471174 | -0.0875352 | -0.1805538 | -0.3659249 | -0.1429387 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.7960898 | 0.3611930 | -0.5761107 | -0.8208543 | 0.0530682 | -0.1048045 | -0.5830273 | 0.4427267 | 0.5694606 | -0.1782323 | -0.2332699 | 0.3403863 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | -0.4393875 | -0.2161697 | -0.4335854 | 0.3311266 | 0.7125600 | 0.2112237 | 0.4176059 | 0.6249394 | 0.1127788 | -0.4698435 | 0.8000856 | 0.5541922 |
| GOCC HEMOGLOBIN COMPLEX | 0.2778327 | 0.6562078 | 0.0872990 | 0.3021787 | 0.4356389 | 0.8603273 | -0.1475597 | 0.8174960 | -0.3171915 | -0.3182571 | 0.1147465 | 0.6242508 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.6210701 | 0.2798895 | -0.5338590 | 0.2556765 | -0.3910878 | 0.3856995 | -0.0208093 | 0.7555147 | -0.5265583 | 0.4437298 | -0.0719194 | 0.7995090 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8241366 | 0.1978879 | -0.8518695 | -0.7085434 | 0.1364475 | -0.2207307 | -0.4832271 | 0.6029493 | 0.3694891 | -0.0879935 | -0.0661022 | -0.0188564 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.2351340 | 0.5244996 | 0.0180807 | 0.3341684 | 0.4404752 | 0.8577642 | -0.0575719 | 0.8268563 | -0.3402781 | -0.1061007 | 0.3234817 | 0.6504675 |
| GOMF UNMETHYLATED CPG BINDING | -0.2278946 | 0.5854914 | 0.0504234 | 0.6651032 | -0.1432499 | 0.6088574 | 0.5111122 | 0.7257349 | 0.3617639 | 0.4910570 | -0.4589858 | 0.3352202 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.2725356 | -0.0086877 | -0.3030851 | 0.2991217 | -0.2341070 | 0.4085101 | -0.7001966 | -0.3327626 | -0.8967786 | -0.7998827 | -0.3957323 | 0.1338819 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | 0.2843078 | -0.3690233 | -0.0441855 | -0.3750977 | -0.2449805 | -0.6357805 | 0.6591812 | -0.3797724 | 0.4770443 | -0.3367759 | 0.7958485 | 0.5628470 |
| GOMF HAPTOGLOBIN BINDING | 0.3458072 | 0.6114203 | 0.0980665 | 0.2878258 | 0.3782820 | 0.8528111 | -0.0348530 | 0.8237372 | -0.2846152 | -0.1976075 | 0.2397260 | 0.6103144 |
| GOBP HYPOXIA INDUCIBLE FACTOR 1ALPHA SIGNALING PATHWAY | 0.4299520 | -0.7090788 | 0.6424026 | 0.0208969 | 0.3817663 | -0.5990869 | 0.3908403 | -0.2389975 | 0.3914491 | 0.3830599 | 0.7427498 | -0.0264327 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.7544277 | 0.1613312 | -0.7247988 | -0.7589730 | -0.4147257 | -0.3606685 | -0.2991274 | 0.4630960 | 0.5809880 | 0.0129963 | -0.0441474 | 0.0957946 |
| GOBP POSITIVE REGULATION OF PYROPTOSIS | 0.3970609 | -0.4186712 | 0.5448709 | -0.4377895 | -0.1985733 | -0.4611119 | 0.5921434 | -0.0875921 | 0.7469920 | 0.3952918 | 0.3012032 | 0.6240453 |
| GOCC CHROMOSOME PASSENGER COMPLEX | -0.5230825 | 0.0067377 | -0.6686166 | 0.1920162 | 0.0284251 | 0.5281081 | 0.1918260 | 0.7446019 | -0.2589334 | 0.7314436 | -0.0756207 | 0.6155395 |
| GOMF LIGAND GATED MONOATOMIC ION CHANNEL ACTIVITY INVOLVED IN REGULATION OF PRESYNAPTIC MEMBRANE POTENTIAL | -0.0818471 | 0.2319209 | -0.5623912 | 0.4787654 | -0.5033433 | 0.4508584 | 0.0275741 | 0.4403196 | -0.4395777 | 0.7460408 | -0.6947353 | 0.1512627 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | -0.1743948 | -0.2625862 | 0.0483093 | -0.3568269 | -0.2249203 | -0.5204642 | 0.5946164 | 0.1137300 | 0.9009654 | 0.6738289 | 0.5560375 | 0.0927284 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.2978693 | 0.1318209 | -0.0288373 | 0.3867275 | 0.4903453 | 0.5435810 | -0.7394654 | 0.0782840 | -0.8857129 | -0.5661086 | 0.0111608 | 0.1117505 |
| GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | -0.6602004 | 0.2783557 | -0.5921862 | -0.7424291 | -0.3036725 | -0.1778359 | -0.3684797 | 0.3767284 | 0.6159538 | 0.0447019 | -0.3028028 | 0.4108918 |
| GOCC BRCA1 C COMPLEX | 0.2448714 | -0.7906085 | 0.4815467 | -0.1958369 | 0.3528171 | -0.7246108 | 0.4315451 | -0.1822188 | -0.1987856 | 0.2955071 | 0.6993881 | -0.1173151 |
| GOCC PROTEASOME CORE COMPLEX ALPHA SUBUNIT COMPLEX | -0.5567997 | -0.2985765 | -0.4864753 | -0.7573637 | 0.3559368 | -0.5302735 | -0.3714557 | -0.0065568 | 0.4413182 | -0.4099677 | 0.4902531 | 0.2899745 |
| GOMF PROTEASOME ACTIVATING ACTIVITY | -0.6326611 | 0.1256540 | -0.6714068 | -0.6503060 | 0.4853832 | -0.2196328 | -0.4206221 | 0.4140746 | 0.5200545 | -0.2677954 | 0.1958210 | 0.3427344 |
| GOCC PICLN SM PROTEIN COMPLEX | -0.6348489 | 0.0356067 | -0.6159358 | -0.7520530 | 0.1518279 | -0.5089730 | -0.4312122 | 0.2477885 | 0.6597546 | -0.1296490 | 0.2615809 | -0.1436317 |
| GOCC SIGNAL PEPTIDASE COMPLEX | -0.6048129 | -0.5276359 | -0.5626766 | -0.4552528 | 0.3505493 | -0.7246588 | -0.1701717 | 0.1555999 | 0.0225329 | -0.3328197 | 0.6439435 | 0.0947829 |
| GOMF NEUROTROPHIN BINDING | -0.1987770 | 0.0564974 | 0.0410328 | 0.3139732 | 0.4994259 | 0.5770477 | -0.6830984 | 0.0214914 | -0.8887990 | -0.6044709 | -0.0274299 | 0.2029353 |
| GOBP GANGLIOSIDE CATABOLIC PROCESS | -0.7325344 | -0.2501831 | -0.5172873 | -0.5184667 | -0.0622343 | -0.5629429 | -0.4432301 | 0.1154230 | -0.1028487 | 0.4305797 | -0.2435440 | -0.6664099 |
| GOCC IMMUNOGLOBULIN COMPLEX CIRCULATING | -0.5751608 | 0.2107373 | -0.6009099 | 0.3288616 | -0.4067750 | 0.2123374 | 0.1589536 | 0.6317535 | -0.3907218 | 0.5008714 | 0.0439517 | 0.6915033 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7505388 | 0.0600660 | -0.7635479 | -0.7016982 | 0.1550503 | -0.2980140 | -0.4259877 | 0.5276578 | 0.3163898 | -0.1004077 | -0.0766651 | -0.0762888 |
| GOBP OXYGEN TRANSPORT | 0.2820284 | 0.4898202 | 0.2309105 | 0.3481305 | 0.4357911 | 0.6833413 | -0.0279326 | 0.7207877 | -0.3113690 | -0.2472648 | 0.3636666 | 0.6105889 |
| GOCC IGM IMMUNOGLOBULIN COMPLEX | -0.3730023 | 0.3857734 | -0.3187904 | 0.2199034 | -0.4647308 | 0.5718108 | -0.1336924 | 0.4724719 | -0.6199463 | 0.1964659 | -0.1469511 | 0.8142004 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.4390831 | -0.0903125 | -0.6257193 | -0.1749655 | -0.5384411 | -0.7428259 | -0.2453702 | 0.3748228 | 0.1638940 | 0.7273410 | 0.2453132 | 0.2018072 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.7551958 | 0.1429512 | -0.8293119 | -0.6376026 | 0.0890367 | -0.2079986 | -0.4604369 | 0.5415137 | 0.2198121 | -0.0683521 | -0.1221788 | -0.0204247 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.6983256 | 0.1448589 | -0.6762940 | -0.7693642 | -0.2926479 | -0.3557167 | -0.2631170 | 0.3719022 | 0.5728911 | -0.0309495 | -0.0134080 | 0.0473168 |
mitch_report(res=mm2,outfile="multigostratified_all_mitchreport.html",overwrite=TRUE)## Dataset saved as " /tmp/Rtmpadl22y/multigostratified_all_mitchreport.rds ".##
##
## processing file: mitch.Rmd## 1/34
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## 29/34 [detailed_geneset_reports1d]
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## 33/34 [session_info]
## 34/34## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/paddi_data/dge/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpadl22y/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 --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --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/Rtmpadl22y/rmarkdown-str3ffac336d8c03a.html##
## Output created: /tmp/Rtmpadl22y/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 | -0.9185365 | 0.5244638 | -0.6907935 | 0.8358838 |
| GOMF UBIQUINOL CYTOCHROME C REDUCTASE ACTIVITY | -0.8370633 | 0.3520429 | -0.7009560 | 0.7519096 |
| GOMF UBIQUITIN LIKE PROTEIN SPECIFIC ENDOPEPTIDASE ACTIVITY | 0.4596661 | -0.9053464 | 0.7725314 | -0.4308713 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.9778642 | -0.1545941 | -0.7811480 | 0.3957283 |
| GOMF LIPID ANTIGEN BINDING | -0.9778642 | -0.1545941 | -0.7811480 | 0.3957283 |
| GOBP PLANAR CELL POLARITY PATHWAY INVOLVED IN NEURAL TUBE CLOSURE | -0.7165508 | 0.6240243 | -0.1201518 | 0.8304061 |
| GOMF INTRAMOLECULAR OXIDOREDUCTASE ACTIVITY INTERCONVERTING ALDOSES AND KETOSES | -0.7786620 | 0.4172765 | -0.4980181 | 0.7419655 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.6374531 | 0.3267427 | -0.5350037 | 0.8563032 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1535513 | 0.6825612 | -0.7345346 | 0.6631329 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C | -0.7704782 | 0.2094750 | -0.5770302 | 0.6398308 |
| GOCC MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX III | -0.7280439 | 0.2918417 | -0.5508335 | 0.6719225 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.8562268 | 0.0607821 | -0.4615870 | 0.6220627 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8278591 | 0.1960384 | -0.4816377 | 0.6093138 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.2459406 | -0.8135663 | 0.7739952 | -0.0046720 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.8006679 | 0.3601281 | -0.5804026 | 0.4508875 |
| GOMF OXIDOREDUCTASE ACTIVITY ACTING ON DIPHENOLS AND RELATED SUBSTANCES AS DONORS | -0.7169388 | 0.1677925 | -0.6913428 | 0.5117027 |
| GOBP POSITIVE REGULATION OF PLASMINOGEN ACTIVATION | -0.7151221 | 0.1834737 | -0.6075300 | 0.5722192 |
| GOBP LIPOXYGENASE PATHWAY | -0.5080229 | 0.3289521 | -0.8836995 | 0.3016483 |
| GOBP GLYCOLYTIC PROCESS THROUGH GLUCOSE 6 PHOSPHATE | -0.6973834 | 0.3673958 | -0.4750747 | 0.6086603 |
| GOCC HEMOGLOBIN COMPLEX | 0.2724611 | 0.6557182 | -0.1457914 | 0.8204941 |
| GOMF UNMETHYLATED CPG BINDING | -0.2374382 | 0.5851327 | 0.5108051 | 0.7294145 |
| GOBP NAD CATABOLIC PROCESS | -0.6328772 | 0.4397462 | -0.5009309 | 0.5887410 |
| GOMF OLIGOSACCHARYL TRANSFERASE ACTIVITY | -0.7906426 | -0.5197805 | -0.1628264 | 0.5146947 |
| GOMF HAPTOGLOBIN BINDING | 0.3396533 | 0.6108430 | -0.0330940 | 0.8265827 |
| GOBP SEQUESTERING OF METAL ION | -0.7584850 | 0.2058709 | -0.4964207 | 0.5051459 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.5363916 | 0.5211459 | -0.6487529 | -0.3578638 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.7598094 | 0.1411377 | -0.4588109 | 0.5474078 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION OF LIPID ANTIGEN VIA MHC CLASS IB | -0.8364491 | -0.1316967 | -0.4769506 | 0.3975993 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.5855337 | 0.2616064 | -0.1336874 | 0.8168177 |
| GOMF FATTY ACYL COA SYNTHASE ACTIVITY | 0.4851681 | -0.2471255 | -0.3138440 | -0.8349508 |
| GOMF PROTON TRANSPORTING ATP SYNTHASE ACTIVITY ROTATIONAL MECHANISM | -0.7645683 | 0.0486009 | -0.4099135 | 0.5795964 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8993277 | 0.1616190 | -0.2666819 | 0.4033753 |
| GOCC RESPIRATORY CHAIN COMPLEX IV | -0.6874828 | 0.1263707 | -0.5258169 | 0.5497712 |
| GOMF ICOSANOID BINDING | -0.2709274 | 0.5220889 | -0.8031900 | 0.2430394 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7549327 | 0.0578276 | -0.4241820 | 0.5339135 |
| GOMF SERINE TYPE CARBOXYPEPTIDASE ACTIVITY | -0.5967254 | -0.4863023 | -0.6560896 | -0.0641482 |
| GOCC CASPASE COMPLEX | -0.7129134 | 0.1703439 | -0.2078740 | 0.6678611 |
| GOCC CYTOCHROME COMPLEX | -0.6608381 | 0.1983774 | -0.5099663 | 0.5344539 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.2288245 | 0.5235452 | -0.0557919 | 0.8296916 |
| GOBP GLYCERALDEHYDE 3 PHOSPHATE METABOLIC PROCESS | -0.6921409 | 0.2034675 | -0.5488289 | 0.4400915 |
| GOCC OLIGOSACCHARYLTRANSFERASE COMPLEX | -0.7767024 | -0.3097652 | -0.0785490 | 0.5525672 |
| GOMF SULFATIDE BINDING | -0.7162406 | -0.1717905 | 0.2148182 | 0.6486622 |
| GOMF PORIN ACTIVITY | -0.7783266 | -0.1799457 | -0.5231431 | 0.3007226 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.5985951 | 0.2980439 | -0.0184546 | 0.7437683 |
| GOBP PROTEIN REPAIR | -0.5853921 | 0.1585261 | -0.7247927 | 0.3260760 |
| GOBP MITOCHONDRIAL ELECTRON TRANSPORT CYTOCHROME C TO OXYGEN | -0.6486414 | 0.1124840 | -0.5228761 | 0.5267863 |
| GOMF SUPEROXIDE GENERATING NADPH OXIDASE ACTIVATOR ACTIVITY | -0.2473102 | 0.5558188 | -0.7735041 | -0.0690302 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.8206756 | 0.1492046 | -0.3484067 | 0.3898440 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.7362331 | 0.2622119 | -0.5439840 | 0.2215819 |
| GOBP MITOCHONDRIAL RESPIRASOME ASSEMBLY | -0.6757340 | -0.1295666 | -0.5148359 | 0.4564724 |
#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 | 0.6967173 | -0.9776848 | -0.8782941 |
| GOMF LARGE RIBOSOMAL SUBUNIT RRNA BINDING | -0.8227698 | -0.9220515 | 0.7377467 | -0.1594617 |
| GOBP ANTIGEN PROCESSING AND PRESENTATION ENDOGENOUS LIPID ANTIGEN VIA MHC CLASS IB | -0.8272620 | -0.7331454 | -0.8693098 | -0.3377467 |
| GOMF LIPID ANTIGEN BINDING | -0.8272620 | -0.7331454 | -0.8693098 | -0.3377467 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | 0.6984814 | 0.5728653 | -0.6586705 | -0.7976721 |
| GOCC CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | -0.7053058 | -0.8656617 | 0.6563245 | 0.0214901 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.7437445 | 0.4235533 | -0.6298063 | 0.7054426 |
| GOBP GLUCURONATE CATABOLIC PROCESS TO XYLULOSE 5 PHOSPHATE | -0.5771028 | -0.6573611 | 0.5938529 | 0.6981904 |
| GOBP SHORT CHAIN FATTY ACID CATABOLIC PROCESS | -0.4734537 | -0.7624093 | 0.6844754 | 0.5539187 |
| GOCC COLLAGEN TYPE IV TRIMER | 0.2623443 | 0.6946986 | -0.8242248 | -0.5627899 |
| GOBP POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO TELOMERE | -0.7827732 | -0.6239301 | 0.6435490 | -0.3290009 |
| GOCC EXTRINSIC COMPONENT OF MITOCHONDRIAL INNER MEMBRANE | -0.6702132 | -0.6578608 | 0.5828976 | 0.5476591 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX CATALYTIC CORE F 1 | -0.7950350 | -0.8188051 | 0.4310448 | -0.1794126 |
| GOBP PROTEIN DEUBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 0.5939920 | 0.7164249 | -0.6227436 | -0.5023720 |
| GOBP REGULATION OF MATRIX METALLOPEPTIDASE SECRETION | 0.3631900 | 0.1029008 | -0.8374102 | -0.8120760 |
| GOMF NITRITE REDUCTASE ACTIVITY | -0.3969445 | 0.3116901 | -0.7238970 | -0.8398884 |
| GOCC EXTERNAL SIDE OF APICAL PLASMA MEMBRANE | 0.2237337 | 0.7345822 | -0.6921888 | -0.6438665 |
| GOBP CANNABINOID SIGNALING PATHWAY | -0.1575118 | 0.3694720 | -0.8711999 | -0.7459206 |
| GOBP SCARNA LOCALIZATION TO CAJAL BODY | -0.7423661 | -0.6362644 | 0.6877330 | -0.1973084 |
| GOCC BASEMENT MEMBRANE COLLAGEN TRIMER | 0.3146910 | 0.7113930 | -0.7854317 | -0.4894285 |
| GOMF UBIQUITIN LIGASE INHIBITOR ACTIVITY | -0.7286848 | -0.7619019 | 0.5900965 | 0.0214542 |
| GOCC ANKYRIN 1 COMPLEX | 0.6183634 | 0.6598008 | -0.1722366 | -0.7735643 |
| GOCC IGE IMMUNOGLOBULIN COMPLEX | -0.8023461 | 0.3879422 | -0.4882241 | 0.6340820 |
| GOBP ISOLEUCINE METABOLIC PROCESS | -0.5195785 | -0.4291950 | 0.7390610 | 0.6547965 |
| GOCC PICLN SM PROTEIN COMPLEX | -0.6200761 | -0.7567105 | 0.6679550 | -0.1213113 |
| GOBP VESTIBULOCOCHLEAR NERVE MORPHOGENESIS | 0.0434482 | -0.3662635 | 0.9036828 | 0.6773302 |
| GOCC MITOCHONDRIAL PROTON TRANSPORTING ATP SYNTHASE COMPLEX COUPLING FACTOR F O | -0.8540725 | -0.7135022 | 0.3808268 | -0.0793579 |
| GOMF STRUCTURAL CONSTITUENT OF RIBOSOME | -0.6746086 | -0.7703332 | 0.5810208 | -0.0213389 |
| GOCC PROTEASOME CORE COMPLEX BETA SUBUNIT COMPLEX | -0.5809814 | -0.8248761 | 0.5795079 | -0.1697030 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.6443939 | 0.4148856 | -0.7558688 | 0.4670709 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 2B COMPLEX | -0.5587342 | -0.7611349 | 0.6836592 | -0.0318996 |
| GOCC CHAPERONIN CONTAINING T COMPLEX | -0.6783993 | -0.6330756 | 0.6043555 | -0.3293012 |
| GOMF THREONINE TYPE ENDOPEPTIDASE ACTIVITY | -0.5968014 | -0.7475316 | 0.6250065 | 0.0530972 |
| GOCC LARGE RIBOSOMAL SUBUNIT | -0.6678855 | -0.7449246 | 0.5453723 | -0.0504911 |
| GOCC BOX C D RNP COMPLEX | -0.6008002 | -0.6856779 | 0.6183141 | -0.2887151 |
| GOCC MITOCHONDRIAL INTERMEMBRANE SPACE PROTEIN TRANSPORTER COMPLEX | -0.7285197 | -0.6906137 | 0.5186802 | 0.1175829 |
| GOCC RIBOSOMAL SUBUNIT | -0.6475190 | -0.7461265 | 0.5510165 | -0.0371054 |
| GOCC METHYLOSOME | -0.6929094 | -0.6554858 | 0.5876275 | -0.1489213 |
| GOCC MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT | -0.7005594 | -0.7268829 | 0.5071784 | 0.0020770 |
| GOCC PROTEASOME CORE COMPLEX | -0.5381061 | -0.7956467 | 0.5128166 | -0.2752074 |
| GOMF C PALMITOYLTRANSFERASE ACTIVITY | 0.2282077 | 0.0594890 | -0.8064199 | -0.7394926 |
| GOMF NERVE GROWTH FACTOR BINDING | -0.0327074 | 0.3816669 | -0.8832962 | -0.5630579 |
| GOMF PROTEASOME ACTIVATING ACTIVITY | -0.6756241 | -0.6569211 | 0.5296534 | -0.2585368 |
| GOBP PROTEIN LOCALIZATION TO NUCLEAR BODY | -0.6626037 | -0.5803657 | 0.6379679 | -0.2209791 |
| GOBP COLLAGEN ACTIVATED TYROSINE KINASE RECEPTOR SIGNALING PATHWAY | 0.0273591 | 0.5198145 | -0.7764246 | -0.5899586 |
| GOBP AMP SALVAGE | -0.4390288 | -0.7894880 | 0.6290625 | -0.0928253 |
| GOBP POSITIVE REGULATION OF PYROPTOSIS | 0.5408748 | -0.4451032 | 0.7502592 | 0.4022733 |
| GOCC PROTON TRANSPORTING ATP SYNTHASE COMPLEX | -0.7663074 | -0.7069017 | 0.3273273 | -0.0919361 |
| GOCC SMALL RIBOSOMAL SUBUNIT | -0.6025433 | -0.7362781 | 0.5430055 | -0.0159655 |
| GOCC EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX EIF3M | -0.5876682 | -0.7762433 | 0.4839682 | -0.1072598 |
#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 | -0.8167545 | -0.8679593 | -0.5666980 | -0.5045745 |
| GOMF LIPID ANTIGEN BINDING | -0.8167545 | -0.8679593 | -0.5666980 | -0.5045745 |
| GOMF HEMOGLOBIN BINDING | 0.4182434 | 0.9148075 | 0.3419669 | 0.8535523 |
| GOCC IGA IMMUNOGLOBULIN COMPLEX | -0.7322925 | 0.3888463 | -0.4245505 | 0.9867269 |
| GOBP ESTABLISHMENT OF MITOTIC SISTER CHROMATID COHESION | 0.8598593 | -0.4605909 | 0.8447573 | -0.0866045 |
| GOCC PHAGOCYTIC VESICLE LUMEN | -0.1420181 | 0.8087349 | -0.8476280 | 0.5200301 |
| GOBP REGULATION OF ENDOPLASMIC RETICULUM TUBULAR NETWORK ORGANIZATION | 0.7613938 | -0.3541363 | 0.8622551 | 0.2545614 |
| GOCC SARCOPLASMIC RETICULUM LUMEN | 0.7106551 | 0.2075866 | 0.8006965 | 0.5553087 |
| GOCC MCRD MEDIATED MRNA STABILITY COMPLEX | 0.5102598 | -0.8345444 | 0.6636483 | -0.3095256 |
| GOBP POSITIVE REGULATION OF CHONDROCYTE PROLIFERATION | -0.6159827 | 0.4056288 | -0.5240211 | 0.8129706 |
| GOCC IGG IMMUNOGLOBULIN COMPLEX | -0.5482653 | 0.4021089 | -0.2222285 | 0.9748246 |
| GOCC HAPTOGLOBIN HEMOGLOBIN COMPLEX | 0.4379590 | 0.8563673 | 0.3238875 | 0.6512166 |
| GOBP INTERLEUKIN 27 MEDIATED SIGNALING PATHWAY | -0.2474684 | -0.6377268 | 0.7959818 | 0.5639784 |
| GOCC GLYCOPROTEIN IB IX V COMPLEX | 0.1345068 | 0.7311370 | -0.8315889 | 0.3585090 |
| GOCC HEMOGLOBIN COMPLEX | 0.4329426 | 0.8589747 | 0.1149084 | 0.6250812 |
| GOCC CRD MEDIATED MRNA STABILITY COMPLEX | 0.7008471 | -0.6343373 | 0.6126318 | -0.2037651 |
| GOMF HAPTOGLOBIN BINDING | 0.3755590 | 0.8515062 | 0.2401859 | 0.6111320 |
| GOBP REGULATION OF CONNECTIVE TISSUE REPLACEMENT | 0.9189947 | 0.0179782 | 0.5683547 | -0.3371423 |
| GOBP NEGATIVE REGULATION OF FIBROBLAST APOPTOTIC PROCESS | 0.8202570 | -0.0018512 | 0.6879089 | 0.3439388 |
| GOBP LOW DENSITY LIPOPROTEIN RECEPTOR PARTICLE METABOLIC PROCESS | 0.5211716 | 0.4956464 | -0.6516528 | -0.5340676 |
| GOCC IGM IMMUNOGLOBULIN COMPLEX | -0.4671687 | 0.5682043 | -0.1469640 | 0.8145799 |
| GOBP OXYGEN TRANSPORT | 0.4330368 | 0.6818717 | 0.3641482 | 0.6114391 |
| GOCC BRCA1 C COMPLEX | 0.3499945 | -0.7261731 | 0.7000988 | -0.1160791 |
| GOCC ANKYRIN 1 COMPLEX | 0.4777485 | 0.7957831 | 0.1882530 | 0.5032568 |
| GOMF INHIBITORY MHC CLASS I RECEPTOR ACTIVITY | 0.4511767 | 0.5039303 | 0.5410685 | 0.6214639 |
| GOBP NITRIC OXIDE TRANSPORT | 0.5596762 | 0.8764872 | 0.0311747 | 0.2002447 |
| GOBP MEIOTIC CYTOKINESIS | 0.5738379 | -0.4136427 | 0.7742740 | 0.1395962 |
| GOBP PLASMA CELL DIFFERENTIATION | 0.7493528 | 0.7323841 | 0.0942810 | -0.0636503 |
| GOBP REGULATION OF COMPLEMENT DEPENDENT CYTOTOXICITY | 0.4685338 | 0.7326194 | 0.3862321 | 0.4201695 |
| GOBP CARBON DIOXIDE TRANSPORT | 0.3254060 | 0.7750412 | 0.1187103 | 0.5940457 |
| GOBP NEGATIVE REGULATION OF DENDRITIC CELL APOPTOTIC PROCESS | 0.2625469 | 0.6440282 | 0.4517501 | 0.6210289 |
| GOCC SIGNAL PEPTIDASE COMPLEX | 0.3474586 | -0.7262425 | 0.6448419 | 0.0964044 |
| GOCC MESSENGER RIBONUCLEOPROTEIN COMPLEX | 0.8082239 | -0.1840103 | 0.2726816 | -0.5535683 |
| GOMF PRIMARY AMINE OXIDASE ACTIVITY | 0.3265556 | -0.1728998 | -0.4199917 | -0.8685198 |
| GOMF SPHINGOSINE 1 PHOSPHATE RECEPTOR ACTIVITY | -0.7491965 | 0.2540983 | -0.4341658 | 0.4976399 |
| GOMF OXYGEN CARRIER ACTIVITY | 0.4098412 | 0.6685914 | 0.3020984 | 0.5897613 |
| GOBP NAIL DEVELOPMENT | -0.0788027 | 0.5531815 | 0.0562688 | 0.8462726 |
| GOBP REGULATION OF ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS | -0.5063441 | 0.6988517 | -0.3715173 | 0.3854104 |
| GOBP INTRACELLULAR GLUTAMATE HOMEOSTASIS | -0.8532756 | -0.4509224 | -0.1163215 | 0.2720821 |
| GOBP CHROMOSOME MOVEMENT TOWARDS SPINDLE POLE | 0.4279820 | 0.0454339 | 0.6501938 | 0.6390235 |
| GOBP POSITIVE REGULATION OF PROTEIN K63 LINKED UBIQUITINATION | 0.6370087 | -0.4565074 | 0.5691104 | -0.2237821 |
| GOCC MITOTIC COHESIN COMPLEX | 0.7081400 | -0.4027380 | 0.5593927 | 0.0433695 |
| GOBP COMPLEMENT DEPENDENT CYTOTOXICITY | 0.3476475 | 0.5611610 | 0.4852907 | 0.5536373 |
| GOBP CRD MEDIATED MRNA STABILIZATION | 0.6133597 | -0.4918420 | 0.5647413 | -0.1418067 |
| GOBP REGULATION OF VASCULAR ASSOCIATED SMOOTH MUSCLE CONTRACTION | 0.6332217 | -0.0937857 | 0.3663076 | -0.6394078 |
| GOCC IMMUNOGLOBULIN COMPLEX | -0.3890226 | 0.3868571 | -0.0664254 | 0.8017088 |
| GOBP L LEUCINE CATABOLIC PROCESS | -0.5403991 | -0.7443524 | 0.2458396 | 0.2028614 |
| GOBP PROTEIN FOLDING IN ENDOPLASMIC RETICULUM | 0.6620931 | -0.1056398 | 0.7040683 | -0.0167935 |
| GOBP ISG15 PROTEIN CONJUGATION | -0.5153041 | -0.7011500 | 0.3893883 | 0.1804961 |
| GOBP ECTODERMAL CELL DIFFERENTIATION | 0.5031142 | 0.6645958 | -0.4442353 | -0.2117005 |
#mitch_report(res=mm2,outfile="multigostratified_pod1_mitchreport.html",overwrite=TRUE)Session information
For reproducibility
sessionInfo()## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] pkgload_1.4.0 GGally_2.2.1
## [3] beeswarm_0.4.0 gtools_3.9.5
## [5] tibble_3.2.1 echarts4r_0.4.5
## [7] xlsx_0.6.5 DT_0.33
## [9] eulerr_7.0.2 ggplot2_3.5.1
## [11] kableExtra_1.4.0 MASS_7.3-61
## [13] mitch_1.17.4 DESeq2_1.44.0
## [15] SummarizedExperiment_1.34.0 Biobase_2.64.0
## [17] MatrixGenerics_1.16.0 matrixStats_1.4.1
## [19] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
## [21] IRanges_2.38.1 S4Vectors_0.42.1
## [23] BiocGenerics_0.50.0 dplyr_1.1.4
## [25] WGCNA_1.73 fastcluster_1.2.6
## [27] dynamicTreeCut_1.63-1 reshape2_1.4.4
## [29] gplots_3.2.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9
## [4] magrittr_2.0.3 farver_2.1.2 rmarkdown_2.28
## [7] zlibbioc_1.50.0 vctrs_0.6.5 memoise_2.0.1.9000
## [10] base64enc_0.1-3 progress_1.2.3 htmltools_0.5.8.1
## [13] S4Arrays_1.4.1 SparseArray_1.4.8 Formula_1.2-5
## [16] sass_0.4.9 bslib_0.8.0 KernSmooth_2.23-24
## [19] htmlwidgets_1.6.4 plyr_1.8.9 impute_1.78.0
## [22] cachem_1.1.0 mime_0.12 lifecycle_1.0.4
## [25] iterators_1.0.14 pkgconfig_2.0.3 Matrix_1.7-0
## [28] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.12
## [31] shiny_1.9.1 digest_0.6.37 colorspace_2.1-1
## [34] AnnotationDbi_1.66.0 Hmisc_5.1-3 RSQLite_2.3.7
## [37] labeling_0.4.3 fansi_1.0.6 httr_1.4.7
## [40] abind_1.4-8 compiler_4.4.1 bit64_4.5.2
## [43] withr_3.0.1 doParallel_1.0.17 htmlTable_2.4.3
## [46] backports_1.5.0 BiocParallel_1.38.0 DBI_1.2.3
## [49] ggstats_0.7.0 highr_0.11 DelayedArray_0.30.1
## [52] caTools_1.18.3 tools_4.4.1 foreign_0.8-87
## [55] httpuv_1.6.15 nnet_7.3-19 glue_1.8.0
## [58] promises_1.3.0 grid_4.4.1 checkmate_2.3.2
## [61] cluster_2.1.6 generics_0.1.3 gtable_0.3.5
## [64] preprocessCore_1.66.0 tidyr_1.3.1 hms_1.1.3
## [67] data.table_1.16.0 xml2_1.3.6 utf8_1.2.4
## [70] XVector_0.44.0 foreach_1.5.2 pillar_1.9.0
## [73] stringr_1.5.1 later_1.3.2 rJava_1.0-11
## [76] splines_4.4.1 lattice_0.22-6 survival_3.7-0
## [79] bit_4.5.0 tidyselect_1.2.1 GO.db_3.19.1
## [82] locfit_1.5-9.10 Biostrings_2.72.1 knitr_1.48
## [85] gridExtra_2.3 svglite_2.1.3 xfun_0.48
## [88] stringi_1.8.4 UCSC.utils_1.0.0 yaml_2.3.10
## [91] xlsxjars_0.6.1 evaluate_1.0.1 codetools_0.2-20
## [94] cli_3.6.3 rpart_4.1.23 xtable_1.8-4
## [97] systemfonts_1.1.0 jquerylib_0.1.4 munsell_0.5.1
## [100] Rcpp_1.0.13 png_0.1-8 parallel_4.4.1
## [103] blob_1.2.4 prettyunits_1.2.0 bitops_1.0-9
## [106] viridisLite_0.4.2 scales_1.3.0 purrr_1.0.2
## [109] crayon_1.5.3 rlang_1.1.4 KEGGREST_1.44.1