get_firehoseData: The get_firehoseData function

In MethylMix: MethylMix: Identifying methylation driven cancer genes

Description

Gets data from TCGA's firehose.

Usage

get_firehoseData(downloadData = TRUE, saveDir = "./",
  TCGA_acronym_uppercase = "LUAD", dataType = "stddata",
  dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE,
  fileType = "tar.gz", gdacURL = "http://gdac.broadinstitute.org/runs/",
  untarUngzip = TRUE, printDisease_abbr = FALSE)

Arguments

downloadData	logical indicating if data should be downloaded (default: TRUE). If false, the url of the desired data is returned.
saveDir	path to directory to save downloaded files.
TCGA_acronym_uppercase	TCGA's cancer site code.
dataType	type of data in TCGA (default: "stddata").
dataFileTag	name of the file to be downloaded (the default is to download RNAseq data, but this can be changed to download other data).
FFPE	logical indicating if FFPE data should be downloaded (default: FALSE).
fileType	type of downloaded file (default: "fileType", other type not admitted at the moment).
gdacURL	gdac url.
untarUngzip	logical indicating if the gzip file downloaded should be untarred (default: TRUE).
printDisease_abbr	if TRUE data is not downloaded but all the possible cancer sites codes are shown (default: FALSE).

Value

DownloadedFile path to directory with downloaded files.

MethylMix documentation built on Nov. 8, 2020, 11:08 p.m.