## ----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()