## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager")) # install.packages("BiocManager") # BiocManager::install("RTCGAToolbox") ## ----------------------------------------------------------------------------- library(RTCGAToolbox) # Valid aliases getFirehoseDatasets() ## ----------------------------------------------------------------------------- # Valid stddata runs getFirehoseRunningDates(last = 3) ## ----------------------------------------------------------------------------- # Valid analysis running dates (will return 3 recent date) getFirehoseAnalyzeDates(last=3) ## ----message=FALSE------------------------------------------------------------ # READ mutation data and clinical data brcaData <- getFirehoseData(dataset="READ", runDate="20160128", forceDownload=TRUE, clinical=TRUE, Mutation=TRUE) ## ----------------------------------------------------------------------------- brcaData ## ----------------------------------------------------------------------------- data(accmini) accmini ## ----------------------------------------------------------------------------- biocExtract(accmini, "RNASeq2Gene") biocExtract(accmini, "CNASNP") ## ----------------------------------------------------------------------------- head(getData(accmini, "clinical")) getData(accmini, "RNASeq2GeneNorm") getData(accmini, "GISTIC", "AllByGene") ## ----------------------------------------------------------------------------- sessionInfo()