Download TCGA Data

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.

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).

Value

No values. It only downloads files.

Details

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

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.

See also

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

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, createTCGA, 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])
#> There were more than one datasets matching the dataSet parameter. 
#> Downloaded only 
#> gdac.broadinstitute.org_ACC.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2015110100.0.0.tar.gz
#> 
#> All matches were 
#> 
#> gdac.broadinstitute.org_ACC.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2015110100.0.0.tar.gz
#> gdac.broadinstitute.org_ACC.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.aux.2015110100.0.0.tar.gz
#> gdac.broadinstitute.org_ACC.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.mage-tab.2015110100.0.0.tar.gz

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