gdcRNADownload: Download RNA data in GDC

Description Usage Arguments Value Author(s) Examples

View source: R/gdcRNADownload.R

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

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gdcRNADownload(manifest = NULL, project.id, data.type,
  directory = "Data", write.manifest = FALSE, method = "gdc-client")

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 'gdc-client'.

Value

Downloaded files in the specified directory

Author(s)

Ruidong Li and Han Qu

Examples

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####### 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')

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.