gdcClinicalDownload {GDCRNATools} | R Documentation

## Download clinical data in GDC

### Description

Download clinical data in GDC either by providing the manifest file or specifying the project id and data type

### Usage

    gdcClinicalDownload(manifest = NULL, project.id, directory = "Clinical",
        write.manifest = FALSE, method = "GenomicDataCommons")

### Arguments

`manifest` | menifest file that is downloaded from the GDC cart. If provided, files whose UUIDs are in the manifest file will be downloaded via gdc-client, otherwise, `project id` argument should be provided to download data automatically. Default is `NULL`
`project.id` | project id in GDC
`directory` | the folder to save downloaded files. Default is `'Clinical'`
`write.manifest` | logical, whether to write out the manifest file
`method` | method that is used to download data. Either `'GenomicDataCommons'` which is a well established method developed in the GenomicDataCommons' package, or alternatively `'gdc-client'` which uses the `gdc-client` tool developed by GDC. Default is `'GenomicDataCommons'`.

### Value

downloaded files in the specified directory

### Author(s)

Ruidong Li and Han Qu

### Examples

    ####### Download Clinical data by manifest file #######
    manifest <- 'Clinical.manifest.txt'
    ## Not run: gdcClinicalDownload(manifest  = manifest,
                        directory = 'Clinical')
    ## End(Not run)

    ####### Download Clinical data by project id #######
    project <- 'TCGA-PRAD'
    ## Not run: gdcClinicalDownload(project.id     = project,
                        write.manifest = TRUE,
                        directory      = 'Clinical')
    ## End(Not run)

[Package GDCRNATools version 1.1.1 Index]