inst/doc/RTNsurvival.R

In RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

## ---- 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()