## ---- eval=TRUE--------------------------------------------------------------- library(RTN) data(stni, package="RTN") ## ---- eval=TRUE--------------------------------------------------------------- summary <- tni.get(stni, what = "summary") ## ---- eval=FALSE-------------------------------------------------------------- # library(RTNsurvival) # data(survival.data) ## ---- eval=TRUE, include=FALSE------------------------------------------------ library(RTNsurvival) data(survival.data) ## ---- eval=TRUE--------------------------------------------------------------- rtns <- tni2tnsPreprocess(stni, survivalData = survival.data, time = 1, event = 2, endpoint = 120, keycovar = c("Grade","Age")) ## ---- eval=TRUE, results='hide'----------------------------------------------- rtns <- tnsGSEA2(rtns) ## ---- eval=FALSE-------------------------------------------------------------- # rtns <- tnsCox(rtns) # tnsPlotCox(rtns) ## ---- eval=TRUE, include=FALSE------------------------------------------------ rtns <- tnsCox(rtns) ## ---- eval=FALSE-------------------------------------------------------------- # rtns <- tnsKM(rtns, sections = 2) # tnsPlotKM(rtns, regs="FOXM1", attribs = list(c("ER+","ER-"),c("PR+","PR-"),c("G1","G2","G3"),"HT")) ## ---- eval=TRUE, include=FALSE------------------------------------------------ rtns <- tnsKM(rtns) ## ---- eval=FALSE-------------------------------------------------------------- # tnsPlotGSEA2(rtns, "MB-5115", regs = "FOXM1") ## ---- eval=TRUE, include=FALSE------------------------------------------------ tnsPlotGSEA2(rtns, "MB-5115", regs = "FOXM1") ## ---- eval = FALSE------------------------------------------------------------ # library(pheatmap) # enrichmentScores <- tnsGet(rtns, "regulonActivity") # survival.data <- tnsGet(rtns, "survivalData") # annotation_col <- survival.data[,c("ER+", "ER-")] # pheatmap(t(enrichmentScores$dif), # annotation_col = annotation_col, # show_colnames = FALSE, # annotation_legend = FALSE) ## ----label='Session information', eval=TRUE, echo=FALSE----------------------- sessionInfo()