get_firehoseData: The get_firehoseData function

Description Usage Arguments Value

View source: R/Download_Preprocess.R

Description

Gets data from TCGA's firehose.

Usage

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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.


gevaertlab/methylmix documentation built on May 25, 2019, 5:25 p.m.