get_firehoseData {MethylMix} | R Documentation

## The get_firehoseData function

### 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.

[Package MethylMix version 2.17.0 Index]