TCGAbiolinks (version 1.2.5)

TCGAdownload: Download the data from TCGA using as reference the output from TCGAquery

Description

The TCGAdownload function will download the data using as reference the the lines of the TCGAquery search result.

There is an option to download the entire tar.gz folder or download specific files using the type parameter or the samples parameter

The outpufiles will be saved into the path parameters. If this path does not exists the package will try to create the directories.

By default, if a sample was already downloaded the function will not download again, unless the force parameter is set to TRUE

Usage

TCGAdownload(data = NULL, path = ".", type = NULL, samples = NULL, force = FALSE)

Arguments

data

The TCGAquery output

path

Directory to save the downloaded data

type

Filter the files that will be downloaded by type. Example:"rsem.genes.results"

samples

List of samples to download data

force

Download files even if it was already downladed? Default: FALSE

Value

Download TCGA data into the given path

See Also

TCGAquery for searching the data to download

TCGAprepare for preparing the data for the user into a Summarized experiment object, or a matrix.

Other data.functions: TCGAprepare, TCGAquery

Examples

samples <- c("TCGA-26-1442-01A-01R-1850-01")
query <- TCGAquery(tumor = "gbm",
                   platform = "IlluminaHiSeq_RNASeqV2",
                   level = "3",
                   samples = samples)
TCGAdownload(query,path = "RNA",
             samples = samples,
             type ="rsem.genes.results")