downloadTCGA: Download TCGA data

In RTCGA: The Cancer Genome Atlas Data Integration

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 http://gdac.broadinstitute.org/. For easy access from R check details below.
dataSet	A part of the name of dataSet to be downloaded from http://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 http://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 http://rtcga.github.io/RTCGA/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 documentation built on Nov. 8, 2020, 5:11 p.m.