## ----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 ) ## ----vignette_data_used,eval=TRUE--------------------------------------------- # load vignette data data( myGOs, package="ViSEAGO" ) ## ----geneList_input,eval=TRUE------------------------------------------------- # load genes identifiants (GeneID,ENS...) background (expressed genes) background<-scan( system.file( "extdata/data/input", "background_L.txt", package = "ViSEAGO" ), quiet=TRUE, what="" ) # load Differentialy Expressed (DE) gene identifiants from lists PregnantvsLactateDE<-scan( system.file( "extdata/data/input", "pregnantvslactateDE.txt", package = "ViSEAGO" ), quiet=TRUE, what="" ) VirginvsLactateDE<-scan( system.file( "extdata/data/input", "virginvslactateDE.txt", package = "ViSEAGO" ), quiet=TRUE, what="" ) VirginvsPregnantDE<-scan( system.file( "extdata/data/input", "virginvspregnantDE.txt", package = "ViSEAGO" ), quiet=TRUE, what="" ) ## ----geneList_input-head,echo=FALSE------------------------------------------- # # show the ten first lines of genes_DE (same as genes_ref) # head(PregnantvsLactateDE) ## ----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---------------------------------------------------------- # # create topGOdata for BP for each list of DE genes # BP_PregnantvsLactate<-ViSEAGO::create_topGOdata( # geneSel=PregnantvsLactateDE, # allGenes=background, # gene2GO=myGENE2GO, # ont="BP", # nodeSize=5 # ) # # BP_VirginvsLactate<-ViSEAGO::create_topGOdata( # geneSel=VirginvsLactateDE, # allGenes=background, # gene2GO=myGENE2GO, # ont="BP", # nodeSize=5 # ) # # BP_VirginvsPregnant<-ViSEAGO::create_topGOdata( # geneSel=VirginvsPregnantDE, # allGenes=background, # gene2GO=myGENE2GO, # ont="BP", # nodeSize=5 # ) ## ----Enrichment_data_tests---------------------------------------------------- # # perform topGO tests # elim_BP_PregnantvsLactate<-topGO::runTest( # BP_PregnantvsLactate, # algorithm ="elim", # statistic = "fisher", # cutOff=0.01 # ) # # elim_BP_VirginvsLactate<-topGO::runTest( # BP_VirginvsLactate, # algorithm ="elim", # statistic = "fisher", # cutOff=0.01 # ) # # elim_BP_VirginvsPregnant<-topGO::runTest( # BP_VirginvsPregnant, # algorithm ="elim", # statistic = "fisher", # cutOff=0.01 # ) ## ----Enrichment_merge--------------------------------------------------------- # # merge topGO results # BP_sResults<-ViSEAGO::merge_enrich_terms( # cutoff=0.01, # Input=list( # PregnantvsLactate=c( # "BP_PregnantvsLactate", # "elim_BP_PregnantvsLactate" # ), # VirginvsLactate=c( # "BP_VirginvsLactate", # "elim_BP_VirginvsLactate" # ), # VirginvsPregnant=c( # "BP_VirginvsPregnant", # "elim_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: topGO - summary:PregnantvsLactate BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7699 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 199 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 Nontrivial_nodes: 8433 VirginvsLactate BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 9583 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 152 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 Nontrivial_nodes: 8457 VirginvsPregnant BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7302 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 243 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 Nontrivial_nodes: 8413 - enrichment pvalue cutoff: PregnantvsLactate : 0.01 VirginvsLactate : 0.01 VirginvsPregnant : 0.01 - enrich GOs (in at least one list): 521 GO terms of 3 conditions. PregnantvsLactate : 199 terms VirginvsLactate : 152 terms VirginvsPregnant : 243 terms" ) ## ----Enrichment_merge_table--------------------------------------------------- # # show table in interactive mode # ViSEAGO::show_table(BP_sResults) ## ----Enrichment_merge_count--------------------------------------------------- # # barchart of significant (or not) GO terms by comparison # ViSEAGO::GOcount(BP_sResults) ## ----Enrichment_merge_interactions-------------------------------------------- # # display intersections # ViSEAGO::Upset( # BP_sResults, # file="upset.xls" # ) ## ----SS_build----------------------------------------------------------------- # # create GO_SS-class object # myGOs<-ViSEAGO::build_GO_SS( # gene2GO=myGENE2GO, # enrich_GO_terms=BP_sResults # ) ## ----SS_compute--------------------------------------------------------------- # # compute Semantic Similarity (SS) # myGOs<-ViSEAGO::compute_SS_distances( # myGOs, # distance="Wang" # ) ## ----SS_build_compute_show---------------------------------------------------- # # display a summary # myGOs ## ----SS_build_compute_display,echo=FALSE,eval=TRUE---------------------------- cat( "- object class: GO_SS - ontology: BP - method: topGO - summary: PregnantvsLactate BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7699 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 199 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 Nontrivial_nodes: 8433 VirginvsLactate BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 9583 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 152 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 Nontrivial_nodes: 8457 VirginvsPregnant BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7302 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 243 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 Nontrivial_nodes: 8413 - enrichment pvalue cutoff: PregnantvsLactate : 0.01 VirginvsLactate : 0.01 VirginvsPregnant : 0.01 - enrich GOs (in at least one list): 521 GO terms of 3 conditions. PregnantvsLactate : 199 terms VirginvsLactate : 152 terms VirginvsPregnant : 243 terms - terms distances: Wang" ) ## ----SS_terms_mdsplot--------------------------------------------------------- # # MDSplot # ViSEAGO::MDSplot(myGOs) ## ----SS_Wang-wardD2----------------------------------------------------------- # # Create GOterms heatmap # Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap( # myGOs, # showIC=FALSE, # showGOlabels =FALSE, # GO.tree=list( # tree=list( # distance="Wang", # aggreg.method="ward.D2" # ), # cut=list( # dynamic=list( # pamStage=TRUE, # pamRespectsDendro=TRUE, # deepSplit=2, # minClusterSize =2 # ) # ) # ), # samples.tree=NULL # ) ## ----SS_Wang-wardD2_heatmap_display------------------------------------------- # # display the heatmap # ViSEAGO::show_heatmap( # Wang_clusters_wardD2, # "GOterms" # ) ## ----SS_Wang-ward.D2_table---------------------------------------------------- # # display table # ViSEAGO::show_table( # Wang_clusters_wardD2 # ) ## ----SS_Wang-ward.D2_mdsplot-------------------------------------------------- # # colored MDSplot # ViSEAGO::MDSplot( # Wang_clusters_wardD2, # "GOterms" # ) ## ----SS_Wang-wardD2_groups---------------------------------------------------- # # calculate semantic similarites between clusters of GO terms # Wang_clusters_wardD2<-ViSEAGO::compute_SS_distances( # Wang_clusters_wardD2, # distance="BMA" # ) ## ----SS_Wang-ward.D2_groups_mdsplot------------------------------------------- # # MDSplot # ViSEAGO::MDSplot( # Wang_clusters_wardD2, # "GOclusters" # ) ## ----SS_Wang-wardD2_groups_heatmap-------------------------------------------- # # GOclusters heatmap # Wang_clusters_wardD2<-ViSEAGO::GOclusters_heatmap( # Wang_clusters_wardD2, # tree=list( # distance="BMA", # aggreg.method="ward.D2" # ) # ) ## ----SS_Wang-ward.D2_groups_heatmap_display----------------------------------- # # display the heatmap # ViSEAGO::show_heatmap( # Wang_clusters_wardD2, # "GOclusters" # ) ## ----SS_Wang-wardD2_groups_show----------------------------------------------- # # display a summary # Wang_clusters_wardD2 ## ----SS_Wang-wardD2_groups_display,echo=FALSE,eval=TRUE----------------------- cat( "- object class: GO_clusters - ontology: BP - method: topGO - summary: PregnantvsLactate BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7699 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_PregnantvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 199 feasible_genes: 14091 feasible_genes_significant: 7044 genes_nodeSize: 5 Nontrivial_nodes: 8433 VirginvsLactate BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 9583 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsLactate description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 152 feasible_genes: 14091 feasible_genes_significant: 8734 genes_nodeSize: 5 Nontrivial_nodes: 8457 VirginvsPregnant BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 available_genes: 15804 available_genes_significant: 7302 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 nodes_number: 8463 edges_number: 19543 elim_BP_VirginvsPregnant description: Bioconductor org.Mm.eg.db 2019-Jul10 test_name: fisher p<0.01 algorithm_name: elim GO_scored: 8463 GO_significant: 243 feasible_genes: 14091 feasible_genes_significant: 6733 genes_nodeSize: 5 Nontrivial_nodes: 8413 - enrichment pvalue cutoff: PregnantvsLactate : 0.01 VirginvsLactate : 0.01 VirginvsPregnant : 0.01 - enrich GOs (in at least one list): 521 GO terms of 3 conditions. PregnantvsLactate : 199 terms VirginvsLactate : 152 terms VirginvsPregnant : 243 terms - terms distances: Wang - clusters distances: BMA - Heatmap: * GOterms: TRUE - GO.tree: tree.distance: Wang tree.aggreg.method: ward.D2 cut.dynamic.pamStage: TRUE cut.dynamic.pamRespectsDendro: TRUE cut.dynamic.deepSplit: 2 cut.dynamic.minClusterSize: 2 number of clusters: 62 clusters min size: 2 clusters mean size: 8 clusters max size: 32 - sample.tree: FALSE * GOclusters: TRUE - tree: distance: BMA aggreg.method: ward.D2" ) ## ----session,eval=TRUE,echo=FALSE--------------------------------------------- sessionInfo()