## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----RGSEA-DOWNLOAD, message=FALSE, warning= FALSE------------------------- library(GEOquery) g4100 <- GDS2eSet(getGEO("GDS4100")) g4102 <- GDS2eSet(getGEO("GDS4102")) ## ----RGSEA-transform------------------------------------------------------- e4102<-exprs(g4102) e4100<-exprs(g4100) ## ----RSGEA-data------------------------------------------------------------ e1<-e4102[,c(1,51)] e2<-e4100[,c(1,2,23,24)] colnames(e1)<-c("tumor", "normal") colnames(e2)<-c("tumor","tumor","normal","normal") ## -------------------------------------------------------------------------- library(RGSEA) data(e1) data(e2) RGSEAfix(e1,e2, queryclasses=colnames(e1), refclasses=colnames(e2), random=20000, featurenum=1000, iteration=100)->test ## -------------------------------------------------------------------------- test[[1]] ## -------------------------------------------------------------------------- RGSEApredict(test[[1]], colnames(e2)) ## -------------------------------------------------------------------------- data(cmap) test2<-RGSEAsd(cmap[,1],cmap[,2:6], queryclasses=colnames(cmap)[1], refclasses=colnames(cmap)[2:6], random=5000, sd=2, iteration=100) test2[[1]]