## ----setup,include=FALSE------------------------------------------------------ # load ViSEAGO and mouse db package library(ViSEAGO) # knitr document options knitr::opts_chunk$set( eval=FALSE,echo=TRUE,fig.pos = 'H', fig.width=6,message=FALSE,comment=NA,warning=FALSE ) ## ----geneList_input,eval=TRUE------------------------------------------------- # load gene identifiants and padj test results from Differential Analysis complete tables PregnantvsLactate<-data.table::fread( system.file( "extdata/data/input", "pregnantvslactate.complete.txt", package = "ViSEAGO" ), select = c("Id","padj") ) VirginvsLactate<-data.table::fread( system.file( "extdata/data/input", "virginvslactate.complete.txt", package = "ViSEAGO" ), select = c("Id","padj") ) VirginvsPregnant<-data.table::fread( system.file( "extdata/data/input", "virginvspregnant.complete.txt", package = "ViSEAGO" ), select = c("Id","padj") ) # rank Id based on statistical value (BH padj in this example) data.table::setorder(PregnantvsLactate,padj) data.table::setorder(VirginvsLactate,padj) data.table::setorder(VirginvsPregnant,padj) ## ----geneList_input-head,echo=FALSE,eval=TRUE--------------------------------- # show the ten first lines of genes_DE (same as genes_ref) PregnantvsLactate ## ----Genomic-ressources------------------------------------------------------- # # connect to Bioconductor # Bioconductor<-ViSEAGO::Bioconductor2GO() # # # load GO annotations from Bioconductor # myGENE2GO<-ViSEAGO::annotate( # "org.Mm.eg.db", # Bioconductor # ) ## ----Genomic-ressources_show-------------------------------------------------- # # display summary # myGENE2GO ## ----Genomic-ressources_display,echo=FALSE,eval=TRUE-------------------------- cat( "- object class: gene2GO - database: Bioconductor - stamp/version: 2019-Jul10 - organism id: org.Mm.eg.db GO annotations: - Molecular Function (MF): 22707 annotated genes with 91986 terms (4121 unique terms) - Biological Process (BP): 23210 annotated genes with 164825 terms (12224 unique terms) - Cellular Component (CC): 23436 annotated genes with 107852 terms (1723 unique terms)" ) ## ----Enrichment_data---------------------------------------------------------- # # perform fgseaMultilevel tests # BP_PregnantvsLactate<-ViSEAGO::runfgsea( # geneSel=PregnantvsLactate, # ont="BP", # gene2GO=myGENE2GO, # method ="fgseaMultilevel", # params = list( # scoreType = "pos", # minSize=5 # ) # ) # # BP_VirginvsLactate<-ViSEAGO::runfgsea( # geneSel=VirginvsLactate, # gene2GO=myGENE2GO, # ont="BP", # method ="fgseaMultilevel", # params = list( # scoreType = "pos", # minSize=5 # ) # ) # # BP_VirginvsPregnant<-ViSEAGO::runfgsea( # geneSel=VirginvsPregnant, # gene2GO=myGENE2GO, # ont="BP", # method ="fgseaMultilevel", # params = list( # scoreType = "pos", # minSize=5 # ) # ) ## ----Enrichment_merge--------------------------------------------------------- # # merge fgsea results # BP_sResults<-ViSEAGO::merge_enrich_terms( # cutoff=0.01, # Input=list( # PregnantvsLactate="BP_PregnantvsLactate", # VirginvsLactate="BP_VirginvsLactate", # VirginvsPregnant="BP_VirginvsPregnant" # ) # ) ## ----Enrichment_merge_show---------------------------------------------------- # # display a summary # BP_sResults ## ----Enrichment_merge_display,echo=FALSE,eval=TRUE---------------------------- cat( "- object class: enrich_GO_terms - ontology: BP - method: fgsea - summary: PregnantvsLactate method : fgseaMultilevel sampleSize : 101 minSize : 5 maxSize : Inf eps : 0 scoreType : pos nproc : 0 gseaParam : 1 BPPARAM : fgseaMultilevel absEps : 101 VirginvsLactate method : fgseaMultilevel sampleSize : 101 minSize : 5 maxSize : Inf eps : 0 scoreType : pos nproc : 0 gseaParam : 1 BPPARAM : fgseaMultilevel absEps : 101 VirginvsPregnant method : fgseaMultilevel sampleSize : 101 minSize : 5 maxSize : Inf eps : 0 scoreType : pos nproc : 0 gseaParam : 1 BPPARAM : fgseaMultilevel absEps : 101- enrichment pvalue cutoff: PregnantvsLactate : 0.01 VirginvsLactate : 0.01 VirginvsPregnant : 0.01 - enrich GOs (in at least one list): 184 GO terms of 3 conditions. PregnantvsLactate : 67 terms VirginvsLactate : 58 terms VirginvsPregnant : 64 terms" )