## ----setup, echo=FALSE----------------------------------------------------- suppressPackageStartupMessages({ library(ToPASeq) library(graphite) }) ## ----lib------------------------------------------------------------------- library(ToPASeq) ## ----loadAirway------------------------------------------------------------ library(airway) data(airway) ## ----processAirway--------------------------------------------------------- airSE <- airway[grep("^ENSG", rownames(airway)),] dim(airSE) assay(airSE)[1:4,1:4] ## ----remove zeros---------------------------------------------------------- airSE <- airway[rowSums(assay(airSE))>0,] dim(airSE) assay(airSE)[1:4,1:4] ## -------------------------------------------------------------------------- group <- ifelse(airway$dex == "trt", 1, 0) table(group) ## ----pwys------------------------------------------------------------------ library(graphite) pwys <- pathways(species="hsapiens", database="kegg")[1:5] pwys ## ----nodes----------------------------------------------------------------- nodes(pwys[[1]]) ## ----mapIDs---------------------------------------------------------------- pwys<-graphite::convertIdentifiers(pwys,"ENSEMBL") nodes(pwys[[1]]) ## ----TopologyGSA----------------------------------------------------------- top<-TopologyGSA(assay(airSE), group, pwys, type="RNASeq", nperm=10) res(top) ## ----DEGraph--------------------------------------------------------------- deg<-DEGraph(assay(airSE), group, pwys, type="RNASeq") res(deg) ## ----clipper--------------------------------------------------------------- cli<-clipper(assay(airSE), group, pwys,type="RNASeq", method="mean", nperm=10) res(cli)$results[[1]] ## ----SPIA------------------------------------------------------------------ spi<-SPIA(assay(airSE), group,pwys , type="RNASeq", logFC.th=-1) res(spi) ## ----TAPPA----------------------------------------------------------------- tap<-TAPPA(assay(airSE), group, pwys, type="RNASeq") res(tap) ## ----PRS------------------------------------------------------------------- Prs<-PRS_wrapper( assay(airSE), group, pwys, type="RNASeq", logFC.th=-1, nperm=10) res(Prs) ## ----PWEA------------------------------------------------------------------ pwe<-PWEA(assay(airSE), group, pwys, type="RNASeq", nperm=10) res(pwe)