--- a
+++ b/man/build_gbm_se.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build_gbm_se.R
+\name{build_gbm_se}
+\alias{build_gbm_se}
+\title{use curatedTCGAData and Brennan metadata to build an annotated GBM MAE}
+\usage{
+build_gbm_se(cache = BiocFileCache::BiocFileCache())
+}
+\arguments{
+\item{cache}{if not NULL, location of BiocFileCache instance}
+}
+\description{
+use curatedTCGAData and Brennan metadata to build an annotated GBM MAE
+}
+\note{
+Will cache the created SummarizedExperiment instance unless told not to.
+`rname` is `"brenn_gbm_se"`.
+}
+\examples{
+gbmse = build_gbm_se()
+
+# check effect of MGMT methylation on survival
+
+xm = gbmse[, gbmse$mgmt_status !="" & gbmse$vital_status !=""]
+library(survival)
+ss = Surv(xm$os_days, 1*(xm$vital_status=="DECEASED"))
+plot(survfit(ss~xm$mgmt_status), lty=1:2)
+legend(1100, .95, lty=c(1,2), legend=c("MGMT methylated", "unmethylated"))
+title("Time-on-study/vital status for 123 GBM patients analyzed in Brennan et al. PMID 24120142")
+survdiff(ss~xm$mgmt_status)
+}