saveRTCGAdata: A function to save data from RTCGAToolbox

In waldronlab/MultiAssayExperiment.TCGA: Pipeline for the integration of multi-omics experiments in Bioconductor

A function to save data from RTCGAToolbox

Description

Saves intermediate data from the GDAC Firehose pipeline via RTCGAToolbox

Usage

saveRTCGAdata(
  runDate = "20160128",
  diseaseCode,
  dataType = c("RNASeqGene", "RNASeq2Gene", "miRNASeqGene", "RNASeq2GeneNorm", "CNASNP",
    "CNVSNP", "CNASeq", "CNACGH", "Methylation", "Mutation", "mRNAArray", "miRNAArray",
    "RPPAArray", "GISTIC"),
  analyzeDate = "20160128",
  directory,
  rawDir = "tmp",
  force = FALSE
)

Arguments

runDate	The GDAC Firehose run date, only '20160128' is available
diseaseCode	A single string indicating TCGA cancer code
dataType	A character vector indicating the assay type(s)
analyzeDate	The GDAC Firehose analyze run date, only '20160128' is available
rawDir	Directory location where to save data from the 'RTCGAToolbox::getFirehoseData' function
force	logical (default FALSE) whether to force redownload of resources
drectory	A single string indicating the directory in which to save intermediary datasets

waldronlab/MultiAssayExperiment.TCGA documentation built on May 19, 2023, 6:06 p.m.