inst/doc/RTCGAToolbox-vignette.R

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

## ----eval=FALSE---------------------------------------------------------------
#  if (!requireNamespace("BiocManager"))
#      install.packages("BiocManager")
#  BiocManager::install("RTCGAToolbox")

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library(RTCGAToolbox)
# Valid aliases
getFirehoseDatasets()

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# 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)

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brcaData

## -----------------------------------------------------------------------------
data(accmini)
accmini

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biocExtract(accmini, "RNASeq2Gene")

biocExtract(accmini, "CNASNP")

## -----------------------------------------------------------------------------
head(getData(accmini, "clinical"))

getData(accmini, "RNASeq2GeneNorm")

getData(accmini, "GISTIC", "AllByGene")

## -----------------------------------------------------------------------------
sessionInfo()