## ----setup, echo=FALSE-------------------------------------------------------- suppressPackageStartupMessages({ library(ToPASeq) library(EnrichmentBrowser) library(graphite) library(BiocStyle) }) ## ----lib---------------------------------------------------------------------- library(ToPASeq) ## ----loadAirway--------------------------------------------------------------- library(airway) data(airway) ## ----processAirway------------------------------------------------------------ airSE <- airway[grep("^ENSG", rownames(airway)),] dim(airSE) assay(airSE)[1:4,1:4] ## ----pdataAirway-------------------------------------------------------------- airSE$GROUP <- ifelse(airway$dex == "trt", 1, 0) table(airSE$GROUP) ## ----pdataAirway2------------------------------------------------------------- airSE$BLOCK <- airway$cell table(airSE$BLOCK) ## ----deAirway----------------------------------------------------------------- library(EnrichmentBrowser) airSE <- deAna(airSE, de.method="edgeR") rowData(airSE, use.names=TRUE) ## ----pwys--------------------------------------------------------------------- library(graphite) pwys <- pathways(species="hsapiens", database="kegg") pwys ## ----nodes-------------------------------------------------------------------- nodes(pwys[[1]]) ## ----mapIDs------------------------------------------------------------------- airSE <- idMap(airSE, org="hsa", from="ENSEMBL", to="ENTREZID") ## ----genes-------------------------------------------------------------------- all <- names(airSE) de.ind <- rowData(airSE)$ADJ.PVAL < 0.01 de <- rowData(airSE)$FC[de.ind] names(de) <- all[de.ind] ## ----nrGenes------------------------------------------------------------------ length(all) length(de) ## ----prs---------------------------------------------------------------------- res <- prs(de, all, pwys[1:100], nperm=100) head(res) ## ----prsWeights--------------------------------------------------------------- ind <- grep("ErbB signaling pathway", names(pwys)) weights <- prsWeights(pwys[[ind]], de, all) weights ## ----maxWeight---------------------------------------------------------------- weights[weights == max(weights)]