## ----results1, include=FALSE-------------------------------------------------- library(PoTRA) library(graphite) library(graph) library(igraph) #devtools::install_github('christophergandrud/repmis') library(repmis) source_data("https://github.com/GenomicsPrograms/example_data/raw/master/PoTRA-vignette.RData") options(warn=-1) humanKEGG <- pathways("hsapiens", "kegg") Pathway.database = humanKEGG results.KEGG <-PoTRA.corN(mydata=mydata,genelist=genelist,Num.sample.normal=113,Num.sample.case=113,Pathway.database=Pathway.database[1:15],PR.quantile=PR.quantile) ## ----results2, include=TRUE--------------------------------------------------- names(results.KEGG) head(results.KEGG$Fishertest.p.value) head(results.KEGG$KStest.p.value) head(results.KEGG$LengthOfPathway) head(results.KEGG$TheNumberOfHubGenes.normal) head(results.KEGG$TheNumberOfHubGenes.case) head(results.KEGG$TheNumberOfEdges.normal) head(results.KEGG$TheNumberOfEdges.case) head(results.KEGG$PathwayName) ## ----results3, include=FALSE-------------------------------------------------- humanReactome<- pathways("hsapiens", "reactome") Pathway.database = humanReactome results.Reactome <-PoTRA.corN(mydata=mydata,genelist=genelist,Num.sample.normal=113,Num.sample.case=113,Pathway.database=Pathway.database[1:15],PR.quantile=PR.quantile) ## ----results4, include=TRUE--------------------------------------------------- names(results.Reactome) head(results.Reactome$Fishertest.p.value) head(results.Reactome$KStest.p.value) head(results.Reactome$LengthOfPathway) head(results.Reactome$TheNumberOfHubGenes.normal) head(results.Reactome$TheNumberOfHubGenes.case) head(results.Reactome$TheNumberOfEdges.normal) head(results.Reactome$TheNumberOfEdges.case) head(results.Reactome$PathwayName) ## ----results5, include=FALSE-------------------------------------------------- humanPathBank <- pathways("hsapiens", "pathbank") Pathway.database = humanPathBank results.PathBank <-PoTRA.corN(mydata=mydata,genelist=genelist,Num.sample.normal=113,Num.sample.case=113,Pathway.database=Pathway.database[1:15],PR.quantile=PR.quantile) ## ----results6, include=TRUE--------------------------------------------------- names(results.PathBank) head(results.PathBank$Fishertest.p.value) head(results.PathBank$KStest.p.value) head(results.PathBank$LengthOfPathway) head(results.PathBank$TheNumberOfHubGenes.normal) head(results.PathBank$TheNumberOfHubGenes.case) head(results.PathBank$TheNumberOfEdges.normal) head(results.PathBank$TheNumberOfEdges.case) head(results.PathBank$PathwayName) ## ----results7, include=FALSE-------------------------------------------------- humanPharmGKB <- pathways("hsapiens", "pharmgkb") Pathway.database = humanPharmGKB results.PharmGKB <-PoTRA.corN(mydata=mydata,genelist=genelist,Num.sample.normal=113,Num.sample.case=113,Pathway.database=Pathway.database[1:15],PR.quantile=PR.quantile) ## ----results8, include=TRUE--------------------------------------------------- names(results.PharmGKB) head(results.PharmGKB$Fishertest.p.value) head(results.PharmGKB$KStest.p.value) head(results.PharmGKB$LengthOfPathway) head(results.PharmGKB$TheNumberOfHubGenes.normal) head(results.PharmGKB$TheNumberOfHubGenes.case) head(results.PharmGKB$TheNumberOfEdges.normal) head(results.PharmGKB$TheNumberOfEdges.case) head(results.PharmGKB$PathwayName) ## ----results9, include=FALSE-------------------------------------------------- FPvalues1 <- c(0.01,0.05,1,0.90,0.01,0.05,0.03) FPvalues2 <- c(0.01,1,1,1,0.94,0.34,0.25) FPvalues3 <- c(0.01,0.01,0.04,0.07,0.01,0.03,0.40) FPvalues4 <- c(0.55,0.21,0.01,0.02,0.01,0.01,0.01) Pathways <- c("Statin Pathway - Generalized, Pharmacokinetics","Atorvastatin/Lovastatin/Simvastatin Pathway","Pharmacokinetics","Pravastatin Pathway","Pharmacokinetics","Fluvastatin Pathway", "Pharmacokinetics") DF <- data.frame(Pathways,FPvalues1,FPvalues2,FPvalues3,FPvalues4) DF$FPvalues1 <- sort(FPvalues1, decreasing=FALSE) DF$FPvalues2 <- sort(FPvalues2, decreasing=FALSE) DF$FPvalues3 <- sort(FPvalues3, decreasing=FALSE) DF$FPvalues4 <- sort(FPvalues4, decreasing=FALSE) DF$Rank1 <- c(1,1,2,3,3,4,5) DF$Rank2 <- c(1,2,3,4,5,5,5) DF$Rank3 <- c(1,1,1,2,3,4,5) DF$Rank4 <- c(1,1,1,1,2,3,4) ## ----results10, include=TRUE-------------------------------------------------- DF ## ----results11, include=FALSE------------------------------------------------- library(metap) library(colr) FE = cgrep(DF, "^FPvalues") data_FE <- as.data.frame(t(FE)) FE_SumLog <- t(sapply(data_FE, function(z) sumlog(z)$p )) FE_SumLogs <- data.frame(t(FE_SumLog)) names(FE_SumLogs) <- c("SumLog_Pval") DF$FE_SumLogs <- FE_SumLogs ## ----results12, include=TRUE-------------------------------------------------- FE_SumLogs ## ----results13, include=FALSE------------------------------------------------- Ranks = cgrep(DF, "^Rank") data_Ranks <- Ranks DF$Average_Rank <- rowMeans(data_Ranks, na.rm = TRUE, dims = 1) DF[2:9] <- NULL ## ----results14, include=TRUE-------------------------------------------------- DF ## ----results15, include=TRUE-------------------------------------------------- sessionInfo()