gdcRNADownload {GDCRNATools} | R Documentation

## Download RNA data in GDC

### Description

Download gene expression quantification and isoform expression quantification data from GDC either by providing the manifest file or by sepcifying the project id and data type

### Usage

    gdcRNADownload(manifest = NULL, project.id, data.type, directory = "Data",
        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` and `data.type` arguments should be provided to download data automatically. Default is `NULL`
`project.id` | project id in GDC
`data.type` | one of `'RNAseq'` and `'miRNAs'`
`directory` | the folder to save downloaded files. Default is `'Data'`
`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 RNA data by menifest file #######
    manifest <- 'RNAseq.manifest.txt'
    ## Not run: gdcRNADownload(manifest=manifest)

    ####### Download RNA data by project id and data type #######
    project <- 'TCGA-PRAD'
    ## Not run: gdcRNADownload(project.id=project, data.type='RNAseq')

[Package GDCRNATools version 1.1.1 Index]