% 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)

}