gdcClinicalDownload: Download clinical 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 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 = "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 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 'gdc-client'.

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)

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