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)


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.
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.
A character specifying a directory into which dataSets will be downloaded.
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'.
Logical - should the downloaded file be untarred. Default is TRUE.
Logical - should the downloaded .tar file be removed after untarring. Default is TRUE.
Logical - should download all datasets matching dataSet parameter or only the first one (without FFPE phrase if possible).


No values. It only downloads files.


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


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


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]) ## ---------------------------------------------