downloadTCGA | R Documentation |
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 )
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 |
destDir |
A character specifying a directory into which |
date |
A |
untarFile |
Logical - should the downloaded file be untarred. Default is |
removeTar |
Logical - should the downloaded |
allDataSets |
Logical - should download all datasets matching |
All cohort names can be checked using: sub( x = names( infoTCGA() ), '-counts', '' )
.
No values. It only downloads files.
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.
Marcin Kosinski, m.p.kosinski@gmail.com
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()
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)
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