library("mitch")
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
# m2.cp.reactome.v2024.1.Mm.symbols.gmt m5.go.v2024.1.Mm.symbols.gmt
reactome <- gmt_import("m2.cp.reactome.v2024.1.Mm.symbols.gmt")
names(reactome) <- gsub("REACTOME_","",names(reactome))
names(reactome) <- gsub("_"," ",names(reactome))
go <- gmt_import("m5.go.v2024.1.Mm.symbols.gmt")
names(go) <- gsub("_"," ",names(go))
# WTvsGAL3KO.tsv
wt_gal3ko <- read.table("WTvsGAL3KO.tsv",header=TRUE,row.names=1 )
wt_gal3ko[which(wt_gal3ko$PValue==0),"PValue"] <- 1e-305
# WTvsMSTTG.tsv
wt_mst1ox <- read.table("WTvsMSTTG.tsv",header=TRUE,row.names=1 )
wt_mst1ox[which(wt_mst1ox$PValue==0),"PValue"] <- 1e-305
# MST1TGvsMST1TGGAL3KO
mst1ox_mst1oxko <- read.table("MST1TGvsMST1TGGAL3KO.tsv",header=TRUE,row.names=1 )
mst1ox_mst1oxko[which(mst1ox_mst1oxko$PValue==0),"PValue"] <- 1e-305
# gene table
gt <- data.frame(rownames(wt_gal3ko))
gt2 <- cbind(gt,do.call(rbind,strsplit(gt[,1],"_")))
gt2[,2]=NULL
head(gt2)
## rownames.wt_gal3ko. 2
## 1 ENSMUSG00000088025_Rprl3 Rprl3
## 2 ENSMUSG00000097431_Gm26782 Gm26782
## 3 ENSMUSG00000087775_Rprl2 Rprl2
## 4 ENSMUSG00000021908_Gm6768 Gm6768
## 5 ENSMUSG00000071470_Ccnb1ip1 Ccnb1ip1
## 6 ENSMUSG00000022193_Psmb5 Psmb5
# import
wt_gal3ko_m <- mitch_import(wt_gal3ko,DEtype="edgeR",geneTable=gt2)
## The input is a single dataframe; one contrast only. Converting
## it to a list for you.
## Note: Mean no. genes in input = 15249
## Note: no. genes in output = 15245
## Note: estimated proportion of input genes in output = 1
wt_mst1ox_m <- mitch_import(wt_mst1ox,DEtype="edgeR",geneTable=gt2)
## The input is a single dataframe; one contrast only. Converting
## it to a list for you.
## Note: Mean no. genes in input = 15249
## Note: no. genes in output = 15245
## Note: estimated proportion of input genes in output = 1
mst1ox_mst1oxko_m <- mitch_import(mst1ox_mst1oxko,DEtype="edgeR",geneTable=gt2)
## The input is a single dataframe; one contrast only. Converting
## it to a list for you.
## Note: Mean no. genes in input = 15249
## Note: no. genes in output = 15245
## Note: estimated proportion of input genes in output = 1
# run mitch with GO sets
wt_gal3ko_go <- mitch_calc(wt_gal3ko_m,go, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
wt_mst1ox_go <- mitch_calc(wt_mst1ox_m,go, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
mst1ox_mst1oxko_go <- mitch_calc(mst1ox_mst1oxko_m,go, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(wt_gal3ko_go$enrichment_result,10)
## set
## 5972 GOMF MHC PROTEIN COMPLEX BINDING
## 5202 GOCC MHC PROTEIN COMPLEX
## 6174 GOMF PLATELET DERIVED GROWTH FACTOR BINDING
## 2932 GOBP POSITIVE REGULATION OF PLATELET ACTIVATION
## 2423 GOBP PEPTIDE ANTIGEN ASSEMBLY WITH MHC PROTEIN COMPLEX
## 5133 GOCC GOLGI LUMEN
## 140 GOBP ANTIGEN PROCESSING AND PRESENTATION VIA MHC CLASS IB
## 2146 GOBP NEGATIVE REGULATION OF SUBSTRATE ADHESION DEPENDENT CELL SPREADING
## 5200 GOCC MHC CLASS I PEPTIDE LOADING COMPLEX
## 6118 GOMF PEPTIDE ANTIGEN BINDING
## setSize pANOVA s.dist p.adjustANOVA
## 5972 11 4.964471e-06 -0.7949682 1.084301e-04
## 5202 17 6.526072e-07 -0.6967969 1.917775e-05
## 6174 11 1.002847e-04 -0.6772769 1.507769e-03
## 2932 10 2.160660e-04 -0.6755497 2.749737e-03
## 2423 10 3.021684e-04 -0.6598490 3.658275e-03
## 5133 14 2.161873e-05 -0.6555615 3.914989e-04
## 140 18 1.599675e-06 -0.6531673 4.024086e-05
## 2146 12 1.006207e-04 -0.6483293 1.509311e-03
## 5200 12 1.048680e-04 -0.6466553 1.562147e-03
## 6118 21 5.757717e-07 -0.6300641 1.731332e-05
head(wt_mst1ox_go$enrichment_result,10)
## set
## 980 GOBP FATTY ACID BETA OXIDATION USING ACYL COA DEHYDROGENASE
## 5245 GOCC NADH DEHYDROGENASE COMPLEX
## 3275 GOBP PROTON MOTIVE FORCE DRIVEN ATP SYNTHESIS
## 6099 GOMF OXIDOREDUCTASE ACTIVITY ACTING ON THE CH CH GROUP OF DONORS WITH A FLAVIN AS ACCEPTOR
## 6022 GOMF NADH DEHYDROGENASE UBIQUINONE ACTIVITY
## 5495 GOCC TRICARBOXYLIC ACID CYCLE HETEROMERIC ENZYME COMPLEX
## 1755 GOBP NADH DEHYDROGENASE COMPLEX ASSEMBLY
## 4902 GOCC ALPHA KETOACID DEHYDROGENASE COMPLEX
## 1603 GOBP MITOCHONDRIAL ELECTRON TRANSPORT NADH TO UBIQUINONE
## 5386 GOCC RESPIRASOME
## setSize pANOVA s.dist p.adjustANOVA
## 980 12 1.492716e-08 -0.9436859 5.483186e-07
## 5245 43 3.003685e-26 -0.9328883 5.884493e-24
## 3275 47 2.323008e-28 -0.9297920 4.844596e-26
## 6099 13 7.293615e-09 -0.9261474 2.875196e-07
## 6022 16 1.705007e-10 -0.9216544 8.818296e-09
## 5495 20 1.269829e-12 -0.9162102 8.827357e-11
## 1755 55 9.844348e-32 -0.9122174 2.545748e-29
## 4902 15 3.727488e-09 -0.8789057 1.515611e-07
## 1603 28 1.349817e-15 -0.8717365 1.229094e-13
## 5386 80 3.580856e-41 -0.8672585 1.543349e-38
head(mst1ox_mst1oxko_go$enrichment_result,10)
## set
## 980 GOBP FATTY ACID BETA OXIDATION USING ACYL COA DEHYDROGENASE
## 3275 GOBP PROTON MOTIVE FORCE DRIVEN ATP SYNTHESIS
## 5245 GOCC NADH DEHYDROGENASE COMPLEX
## 1604 GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C
## 6029 GOMF NATURAL KILLER CELL LECTIN LIKE RECEPTOR BINDING
## 6099 GOMF OXIDOREDUCTASE ACTIVITY ACTING ON THE CH CH GROUP OF DONORS WITH A FLAVIN AS ACCEPTOR
## 5201 GOCC MHC CLASS I PROTEIN COMPLEX
## 5386 GOCC RESPIRASOME
## 1603 GOBP MITOCHONDRIAL ELECTRON TRANSPORT NADH TO UBIQUINONE
## 60 GOBP AEROBIC ELECTRON TRANSPORT CHAIN
## setSize pANOVA s.dist p.adjustANOVA
## 980 12 4.124763e-08 0.9142213 1.017809e-06
## 3275 47 3.330618e-23 0.8356167 6.728888e-21
## 5245 43 3.046845e-21 0.8330269 4.804355e-19
## 1604 12 6.775967e-07 0.8280050 1.237475e-05
## 6029 12 8.100747e-07 -0.8222171 1.450729e-05
## 6099 13 3.083815e-07 0.8196408 6.153354e-06
## 5201 10 8.168627e-06 -0.8144798 1.138150e-04
## 5386 80 9.167709e-36 0.8059446 5.926924e-33
## 1603 28 2.242039e-13 0.8002469 1.380456e-11
## 60 59 4.412683e-26 0.7941324 1.188667e-23
nrow(subset(wt_gal3ko_go$enrichment_result,p.adjustANOVA<0.05))
## [1] 1080
nrow(subset(wt_mst1ox_go$enrichment_result,p.adjustANOVA<0.05))
## [1] 1229
nrow(subset(mst1ox_mst1oxko_go$enrichment_result,p.adjustANOVA<0.05))
## [1] 1561
mitch_report(res=wt_gal3ko_go,outfile="wt_gal3ko_go.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/wt_gal3ko_go.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
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## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f026ef89519.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
mitch_report(res=wt_mst1ox_go,outfile="wt_mst1ox_go.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/wt_mst1ox_go.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
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## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f025d3b066.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
mitch_report(res=mst1ox_mst1oxko_go,outfile="mst1ox_mst1oxko_go.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/mst1ox_mst1oxko_go.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
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## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f02181dacdc.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
# run mitch with reactome sets
wt_gal3ko_re <- mitch_calc(wt_gal3ko_m,reactome, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
wt_mst1ox_re <- mitch_calc(wt_mst1ox_m,reactome, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
mst1ox_mst1oxko_re <- mitch_calc(mst1ox_mst1oxko_m,reactome, cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(wt_gal3ko_re$enrichment_result,10)
## set setSize
## 217 ENDOSOMAL VACUOLAR PATHWAY 10
## 231 ER PHAGOSOME PATHWAY 19
## 280 GENERATION OF SECOND MESSENGER MOLECULES 12
## 351 INITIAL TRIGGERING OF COMPLEMENT 13
## 473 NCAM1 INTERACTIONS 16
## 610 RAP1 SIGNALLING 15
## 679 RHO GTPASES ACTIVATE KTN1 10
## 44 ANTIGEN PROCESSING CROSS PRESENTATION 72
## 660 RETROGRADE NEUROTROPHIN SIGNALLING 10
## 67 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 19
## pANOVA s.dist p.adjustANOVA
## 217 1.741564e-04 -0.6854742 1.801618e-03
## 231 9.268831e-05 -0.5179921 1.112260e-03
## 280 1.891205e-03 -0.5179654 1.251533e-02
## 351 1.500525e-03 -0.5085145 1.068104e-02
## 473 5.227461e-04 -0.5008865 4.396930e-03
## 610 9.011348e-04 -0.4950668 6.815306e-03
## 679 6.990196e-03 -0.4926026 3.526246e-02
## 44 1.839173e-12 -0.4802152 3.310511e-10
## 660 9.128015e-03 -0.4761536 4.323797e-02
## 67 5.472087e-04 -0.4580600 4.560072e-03
head(wt_mst1ox_re$enrichment_result,10)
## set setSize pANOVA
## 141 COMPLEX I BIOGENESIS 58 5.552755e-33
## 124 CITRIC ACID CYCLE TCA CYCLE 33 1.138948e-18
## 82 BRANCHED CHAIN AMINO ACID CATABOLISM 20 7.667006e-12
## 882 UBIQUINOL BIOSYNTHESIS 11 5.025280e-07
## 591 PROTEIN LIPOYLATION 10 2.804835e-06
## 658 RESPIRATORY ELECTRON TRANSPORT 124 1.763032e-59
## 139 COMPLEX III ASSEMBLY 17 3.211499e-09
## 415 MATURATION OF TCA ENZYMES AND REGULATION OF TCA CYCLE 18 1.118140e-09
## 449 MITOCHONDRIAL FATTY ACID BETA OXIDATION 33 2.487310e-16
## 30 AEROBIC RESPIRATION AND RESPIRATORY ELECTRON TRANSPORT 202 3.088775e-83
## s.dist p.adjustANOVA
## 141 -0.9065875 9.994959e-31
## 124 -0.8864015 1.138948e-16
## 82 -0.8836125 3.833503e-10
## 882 -0.8748255 1.103110e-05
## 591 -0.8553331 5.609669e-05
## 658 -0.8431342 7.933646e-57
## 139 -0.8290765 1.032268e-07
## 415 -0.8290099 3.727133e-08
## 449 -0.8237715 2.035072e-14
## 30 -0.7856692 2.779898e-80
head(mst1ox_mst1oxko_re$enrichment_result,10)
## set setSize pANOVA
## 217 ENDOSOMAL VACUOLAR PATHWAY 10 2.255354e-06
## 591 PROTEIN LIPOYLATION 10 6.850828e-06
## 139 COMPLEX III ASSEMBLY 17 1.004461e-08
## 82 BRANCHED CHAIN AMINO ACID CATABOLISM 20 2.745599e-09
## 141 COMPLEX I BIOGENESIS 58 5.142162e-24
## 450 MITOCHONDRIAL IRON SULFUR CLUSTER BIOGENESIS 10 3.062275e-05
## 449 MITOCHONDRIAL FATTY ACID BETA OXIDATION 33 2.009804e-13
## 658 RESPIRATORY ELECTRON TRANSPORT 124 2.202680e-45
## 124 CITRIC ACID CYCLE TCA CYCLE 33 6.563266e-13
## 415 MATURATION OF TCA ENZYMES AND REGULATION OF TCA CYCLE 18 1.336824e-07
## s.dist p.adjustANOVA
## 217 -0.8634460 4.720508e-05
## 591 0.8213325 1.284530e-04
## 139 0.8024382 3.476982e-07
## 82 0.7677635 1.074365e-07
## 141 0.7664518 9.255892e-22
## 450 0.7612077 4.374679e-04
## 449 0.7387230 1.507353e-11
## 658 0.7336944 6.608039e-43
## 124 0.7226751 4.219243e-11
## 415 0.7178185 4.296935e-06
nrow(subset(wt_gal3ko_re$enrichment_result,p.adjustANOVA<0.05))
## [1] 195
nrow(subset(wt_mst1ox_re$enrichment_result,p.adjustANOVA<0.05))
## [1] 135
nrow(subset(mst1ox_mst1oxko_re$enrichment_result,p.adjustANOVA<0.05))
## [1] 201
mitch_report(res=wt_gal3ko_re,outfile="wt_gal3ko_re.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/wt_gal3ko_re.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
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## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f021f8cf37d.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
mitch_report(res=wt_mst1ox_re,outfile="wt_mst1ox_re.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/wt_mst1ox_re.rds ".
##
##
## processing file: mitch.Rmd
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## 33/34 [session_info]
## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f0217bc54ce.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
mitch_report(res=mst1ox_mst1oxko_re,outfile="mst1ox_mst1oxko_re.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/mst1ox_mst1oxko_re.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
## 2/34 [checklibraries]
## 3/34
## 4/34 [peek]
## 5/34
## 6/34 [metrics]
## 7/34
## 8/34 [scatterplot]
## 9/34
## 10/34 [contourplot]
## 11/34
## 12/34 [input_geneset_metrics1]
## 13/34
## 14/34 [input_geneset_metrics2]
## 15/34
## 16/34 [input_geneset_metrics3]
## 17/34
## 18/34 [echart1d]
## 19/34 [echart2d]
## 20/34
## 21/34 [heatmap]
## 22/34
## 23/34 [effectsize]
## 24/34
## 25/34 [results_table]
## 26/34
## 27/34 [results_table_complete]
## 28/34
## 29/34 [detailed_geneset_reports1d]
## 30/34
## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f021f813346.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
# run multimitch
mylist <- list("wt_gal3ko"=wt_gal3ko,"wt_mst1ox"=wt_mst1ox,"mst1ox_mst1oxko"=mst1ox_mst1oxko)
multi <- mitch_import(mylist,DEtype="edgeR",geneTable=gt2)
## Note: Mean no. genes in input = 15249
## Note: no. genes in output = 15245
## Note: estimated proportion of input genes in output = 1
multi_go <- mitch_calc(x=multi,genesets=go,cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(multi_go$enrichment_result,20)
## set
## 980 GOBP FATTY ACID BETA OXIDATION USING ACYL COA DEHYDROGENASE
## 5245 GOCC NADH DEHYDROGENASE COMPLEX
## 3275 GOBP PROTON MOTIVE FORCE DRIVEN ATP SYNTHESIS
## 6099 GOMF OXIDOREDUCTASE ACTIVITY ACTING ON THE CH CH GROUP OF DONORS WITH A FLAVIN AS ACCEPTOR
## 5386 GOCC RESPIRASOME
## 6022 GOMF NADH DEHYDROGENASE UBIQUINONE ACTIVITY
## 1604 GOBP MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C
## 1602 GOBP MITOCHONDRIAL ELECTRON TRANSPORT CYTOCHROME C TO OXYGEN
## 5387 GOCC RESPIRATORY CHAIN COMPLEX IV
## 1755 GOBP NADH DEHYDROGENASE COMPLEX ASSEMBLY
## 60 GOBP AEROBIC ELECTRON TRANSPORT CHAIN
## 5032 GOCC CYTOCHROME COMPLEX
## 1603 GOBP MITOCHONDRIAL ELECTRON TRANSPORT NADH TO UBIQUINONE
## 5221 GOCC MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX III
## 5201 GOCC MHC CLASS I PROTEIN COMPLEX
## 5495 GOCC TRICARBOXYLIC ACID CYCLE HETEROMERIC ENZYME COMPLEX
## 179 GOBP ATP SYNTHESIS COUPLED ELECTRON TRANSPORT
## 6021 GOMF NADH DEHYDROGENASE ACTIVITY
## 6029 GOMF NATURAL KILLER CELL LECTIN LIKE RECEPTOR BINDING
## 261 GOBP BRANCHED CHAIN AMINO ACID CATABOLIC PROCESS
## setSize pMANOVA s.wt_gal3ko s.wt_mst1ox s.mst1ox_mst1oxk p.wt_gal3ko
## 980 12 3.426896e-10 -0.19581391 -0.9436859 0.9142213 2.402544e-01
## 5245 43 3.568675e-33 0.31207338 -0.9328883 0.8330269 4.002678e-04
## 3275 47 6.421535e-36 0.29170692 -0.9297920 0.8356167 5.424282e-04
## 6099 13 2.084808e-10 -0.30108678 -0.9261474 0.8196408 6.018454e-02
## 5386 80 8.157503e-57 0.34971316 -0.8672585 0.8059446 6.457531e-08
## 6022 16 2.329879e-11 0.23184385 -0.9216544 0.7871003 1.084158e-01
## 1604 12 1.266554e-08 0.47032758 -0.7788026 0.8280050 4.787548e-03
## 1602 15 1.117969e-10 0.48736266 -0.8263252 0.7593434 1.083013e-03
## 5387 22 2.061451e-15 0.46257159 -0.8214484 0.7731065 1.727902e-04
## 1755 55 9.697151e-38 0.19587049 -0.9122174 0.7781148 1.202148e-02
## 60 59 2.702058e-40 0.34263048 -0.8491943 0.7941324 5.345632e-06
## 5032 33 1.125690e-22 0.47420298 -0.8002534 0.7689623 2.423260e-06
## 1603 28 9.330857e-19 0.22463598 -0.8717365 0.8002469 3.969534e-02
## 5221 12 2.863847e-08 0.46931005 -0.7788573 0.7881026 4.879441e-03
## 5201 10 4.474539e-07 -0.62404989 0.5889071 -0.8144798 6.324205e-04
## 5495 20 1.740854e-12 0.12617406 -0.9162102 0.6760525 3.287504e-01
## 179 69 4.748165e-41 0.32284194 -0.7965533 0.7351386 3.558751e-06
## 6021 11 1.070711e-06 0.32028835 -0.8341748 0.6907038 6.588522e-02
## 6029 12 7.509553e-08 -0.59376573 0.4756122 -0.8222171 3.685443e-04
## 261 20 2.074108e-11 0.08526765 -0.8259442 0.7319278 5.092554e-01
## p.wt_mst1ox p.mst1ox_mst1oxk s.dist SD p.adjustMANOVA
## 980 1.492716e-08 4.124763e-08 1.328415 0.9348181 6.205850e-09
## 5245 3.003685e-26 3.046845e-21 1.289032 0.9073568 5.627192e-31
## 3275 2.323008e-28 3.330618e-23 1.283690 0.9041170 1.064493e-33
## 6099 7.293615e-09 3.083815e-07 1.272876 0.8845439 3.850938e-09
## 5386 3.580856e-41 9.167709e-36 1.234497 0.8649447 4.394854e-54
## 6022 1.705007e-10 4.965566e-08 1.233988 0.8716565 5.004209e-10
## 1604 2.978955e-06 6.775967e-07 1.230176 0.8436123 1.819616e-07
## 1602 2.977272e-08 3.523071e-07 1.223494 0.8479480 2.157513e-09
## 5387 2.506516e-11 3.390999e-10 1.219198 0.8453544 7.404045e-14
## 1755 9.844348e-32 1.643099e-23 1.214894 0.8586899 1.843885e-35
## 60 1.333215e-29 4.412683e-26 1.212094 0.8490017 6.469928e-38
## 5032 1.700822e-15 2.017594e-14 1.206887 0.8340224 8.561863e-21
## 1603 1.349817e-15 2.242039e-13 1.204484 0.8494007 4.569999e-17
## 5221 2.974194e-06 2.266310e-06 1.203319 0.8281419 3.740358e-07
## 5201 1.260587e-03 8.168627e-06 1.183058 0.7612515 4.734516e-06
## 5495 1.269829e-12 1.648352e-07 1.145604 0.8087266 4.379229e-11
## 179 2.140799e-30 4.047495e-26 1.130996 0.7925817 1.334647e-38
## 6021 1.654144e-06 7.276526e-05 1.129382 0.7953246 1.053599e-05
## 6029 4.335001e-03 8.100747e-07 1.120181 0.6928347 9.194935e-07
## 261 1.581427e-10 1.442305e-08 1.106875 0.7826708 4.484652e-10
nrow(subset(multi_go$enrichment_result,p.adjustMANOVA<0.05))
## [1] 2275
mitch_report(res=multi_go,outfile="multi_go.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/multi_go.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
## 2/34 [checklibraries]
## 3/34
## 4/34 [peek]
## 5/34
## 6/34 [metrics]
## 7/34
## 8/34 [scatterplot]
## 9/34
## 10/34 [contourplot]
## 11/34
## 12/34 [input_geneset_metrics1]
## 13/34
## 14/34 [input_geneset_metrics2]
## 15/34
## 16/34 [input_geneset_metrics3]
## 17/34
## 18/34 [echart1d]
## 19/34 [echart2d]
## 20/34
## 21/34 [heatmap]
## 22/34
## 23/34 [effectsize]
## 24/34
## 25/34 [results_table]
## 26/34
## 27/34 [results_table_complete]
## 28/34
## 29/34 [detailed_geneset_reports1d]
## 30/34
## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpiyZ1VC/rmarkdown-str333f02246bafb9.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
multi_re <- mitch_calc(x=multi,genesets=reactome,cores=8,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(multi_re$enrichment_result,20)
## set setSize
## 217 ENDOSOMAL VACUOLAR PATHWAY 10
## 141 COMPLEX I BIOGENESIS 58
## 591 PROTEIN LIPOYLATION 10
## 139 COMPLEX III ASSEMBLY 17
## 82 BRANCHED CHAIN AMINO ACID CATABOLISM 20
## 124 CITRIC ACID CYCLE TCA CYCLE 33
## 658 RESPIRATORY ELECTRON TRANSPORT 124
## 449 MITOCHONDRIAL FATTY ACID BETA OXIDATION 33
## 882 UBIQUINOL BIOSYNTHESIS 11
## 415 MATURATION OF TCA ENZYMES AND REGULATION OF TCA CYCLE 18
## 450 MITOCHONDRIAL IRON SULFUR CLUSTER BIOGENESIS 10
## 30 AEROBIC RESPIRATION AND RESPIRATORY ELECTRON TRANSPORT 202
## 452 MITOCHONDRIAL TRANSLATION 87
## 150 CROSSLINKING OF COLLAGEN FIBRILS 18
## 451 MITOCHONDRIAL PROTEIN DEGRADATION 70
## 74 BETA OXIDATION OF VERY LONG CHAIN FATTY ACIDS 11
## 140 COMPLEX IV ASSEMBLY 38
## 134 COLLAGEN CHAIN TRIMERIZATION 34
## 330 HEME BIOSYNTHESIS 12
## 473 NCAM1 INTERACTIONS 16
## pMANOVA s.wt_gal3ko s.wt_mst1ox s.mst1ox_mst1oxk p.wt_gal3ko
## 217 7.635582e-08 -0.68547424 0.5499442 -0.8634460 1.741564e-04
## 141 5.306638e-39 0.18871403 -0.9065875 0.7664518 1.296909e-02
## 591 1.193824e-06 0.03186085 -0.8553331 0.8213325 8.615216e-01
## 139 4.918035e-11 0.26436595 -0.8290765 0.8024382 5.918009e-02
## 82 5.565709e-13 0.16400657 -0.8836125 0.7677635 2.042680e-01
## 124 1.618500e-20 0.15511279 -0.8864015 0.7226751 1.231671e-01
## 658 1.518749e-74 0.20577343 -0.8431342 0.7336944 7.707120e-05
## 449 8.219842e-19 0.05581718 -0.8237715 0.7387230 5.790795e-01
## 882 6.385530e-07 -0.29150107 -0.8748255 0.6018833 9.415388e-02
## 415 3.448302e-10 0.09650985 -0.8290099 0.7178185 4.784929e-01
## 450 2.102677e-05 0.16550049 -0.7304496 0.7612077 3.648702e-01
## 30 1.782117e-101 0.17610178 -0.7856692 0.6527460 1.652967e-05
## 452 7.759373e-43 0.03830002 -0.7773809 0.6701988 5.372737e-01
## 150 6.677075e-09 -0.34009034 0.6924396 -0.6757879 1.249955e-02
## 451 5.269094e-32 0.06608990 -0.7614818 0.6279445 3.393409e-01
## 74 5.656368e-05 0.01694774 -0.6704143 0.7005741 9.224768e-01
## 140 1.802214e-16 0.22609394 -0.7088979 0.6161394 1.590691e-02
## 134 9.660585e-15 -0.33990494 0.7334050 -0.4717329 6.048689e-04
## 330 4.814730e-05 -0.05912602 -0.6815685 0.6289963 7.228982e-01
## 473 6.116079e-07 -0.50088647 0.6191723 -0.4649271 5.227461e-04
## p.wt_mst1ox p.mst1ox_mst1oxk s.dist SD p.adjustMANOVA
## 217 2.600620e-03 2.255354e-06 1.2320116 0.7698057 1.205618e-06
## 141 5.552755e-33 5.142162e-24 1.2020658 0.8497575 9.551949e-37
## 591 2.804835e-06 6.850828e-06 1.1862533 0.8388073 1.432589e-05
## 139 3.211499e-09 1.004461e-08 1.1837078 0.8313622 1.134931e-09
## 82 7.667006e-12 2.745599e-09 1.1820026 0.8355708 1.615851e-11
## 124 1.138948e-18 6.563266e-13 1.1541347 0.8160889 1.324227e-18
## 658 1.763032e-59 2.202680e-45 1.1364530 0.8026307 4.556247e-72
## 449 2.487310e-16 2.009804e-13 1.1078929 0.7833077 5.284184e-17
## 882 5.025280e-07 5.468274e-04 1.1011612 0.7437598 8.209967e-06
## 415 1.118140e-09 1.336824e-07 1.1008337 0.7783839 7.053345e-09
## 450 6.327649e-05 3.062275e-05 1.0678878 0.7508479 1.802294e-04
## 30 3.088775e-83 8.163806e-58 1.0365159 0.7327154 1.603905e-98
## 452 3.758092e-36 2.882071e-27 1.0271098 0.7257317 1.745859e-40
## 150 3.635653e-07 6.881679e-07 1.0255844 0.7130752 1.155648e-07
## 451 2.719542e-28 9.865125e-20 0.9892101 0.6989350 5.269094e-30
## 74 1.178926e-04 5.727193e-05 0.9698178 0.6854950 3.915947e-04
## 140 3.848991e-14 4.882226e-11 0.9660655 0.6809392 7.723773e-15
## 134 1.313376e-13 1.932750e-06 0.9359221 0.6610258 3.344049e-13
## 330 4.340089e-05 1.612553e-04 0.9293373 0.6555566 3.551850e-04
## 473 1.799311e-05 1.283239e-03 0.9221816 0.6365396 7.977495e-06
nrow(subset(multi_go$enrichment_result,p.adjustMANOVA<0.05))
## [1] 2275
mitch_report(res=multi_re,outfile="multi_re.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpiyZ1VC/multi_re.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
## 2/34 [checklibraries]
## 3/34
## 4/34 [peek]
## 5/34
## 6/34 [metrics]
## 7/34
## 8/34 [scatterplot]
## 9/34
## 10/34 [contourplot]
## 11/34
## 12/34 [input_geneset_metrics1]
## 13/34
## 14/34 [input_geneset_metrics2]
## 15/34
## 16/34 [input_geneset_metrics3]
## 17/34
## 18/34 [echart1d]
## 19/34 [echart2d]
## 20/34
## 21/34 [heatmap]
## 22/34
## 23/34 [effectsize]
## 24/34
## 25/34 [results_table]
## 26/34
## 27/34 [results_table_complete]
## 28/34
## 29/34 [detailed_geneset_reports1d]
## 30/34
## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34
## output file: /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS /home/mark.ziemann@domain.internal.burnet.edu.au/projects/du_lipid_paper/old_analysis/edgeR/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiyZ1VC/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/RtmpiyZ1VC/rmarkdown-str333f0252e3896c.html
##
## Output created: /tmp/RtmpiyZ1VC/mitch_report.html
## [1] TRUE
# GAL3KOvsMST1TGGAL3KO.tsv
# MST1TGvsMST1TGGAL3KO.tsv
# WTvsGAL3KO.tsv
# WTvsMST1TGandMST1TGGAL3KO.tsv
# WTvsMST1TGGAL3KO.tsv
# WTvsMSTTG.tsv