gdcRNADownload: Download RNA data in GDC

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA 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 = "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

####### 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.