get_firehoseData {MethylMix} | R Documentation |
Gets data from TCGA's firehose.
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)
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). |
DownloadedFile path to directory with downloaded files.