downloadTCGA: Download TCGA Data

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

Download TCGA Data

Description

Enables to download TCGA data from specified dates of releases of concrete Cohorts of cancer types. Pass a name of required dataset to the dataSet parameter. By default the Merged Clinical dataSet is downloaded (value dataSet = 'Merge_Clinical.Level_1') from the newest available date of the release.

Usage

downloadTCGA(
  cancerTypes,
  dataSet = "Merge_Clinical.Level_1",
  destDir,
  date = NULL,
  untarFile = TRUE,
  removeTar = TRUE,
  allDataSets = FALSE
)

Arguments

cancerTypes	A character vector containing abbreviations (Cohort code) of types of cancers to download from https://gdac.broadinstitute.org/. For easy access from R check details below.
dataSet	A part of the name of dataSet to be downloaded from https://gdac.broadinstitute.org/runs/. By default the Merged Clinical dataSet is downloaded (value dataSet = 'Merge_Clinical.Level_1'). Available datasets' names can be checked using checkTCGA function.
destDir	A character specifying a directory into which dataSets will be downloaded.
date	A NULL or character specifying from which date dataSets should be downloaded. By default (date = NULL) the newest available date is used. All available dates can be checked on https://gdac.broadinstitute.org/runs/ or by using checkTCGA function. Required format 'YYYY-MM-DD'.
untarFile	Logical - should the downloaded file be untarred. Default is TRUE.
removeTar	Logical - should the downloaded .tar file be removed after untarring. Default is TRUE.
allDataSets	Logical - should download all datasets matching dataSet parameter or only the first one (without FFPE phrase if possible).

Details

All cohort names can be checked using: sub( x = names( infoTCGA() ), '-counts', '' ).

Value

No values. It only downloads files.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

Author(s)

Marcin Kosinski, [e-mail]

See Also

RTCGA website https://rtcga.github.io/RTCGA/articles/Data_Download.html.

Other RTCGA: RTCGA-package, boxplotTCGA(), checkTCGA(), convertTCGA(), datasetsTCGA, expressionsTCGA(), heatmapTCGA(), infoTCGA(), installTCGA(), kmTCGA(), mutationsTCGA(), pcaTCGA(), readTCGA(), survivalTCGA(), theme_RTCGA()

Examples

dir.create('hre')

downloadTCGA(cancerTypes = 'ACC',
             dataSet = 'miR_gene_expression',
             destDir = 'hre',
             date = tail(checkTCGA('Dates'), 2)[1])

## Not run: 
downloadTCGA(cancerTypes = c('BRCA', 'OV'),
             destDir = 'hre',
             date = tail(checkTCGA('Dates'), 2)[1])

## End(Not run)

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.