Download a TCGA RNA-seq dataset

Queries, downloads and prepares a TCGA gene-expression dataset (STAR counts) via TCGAbiolinks, saving the prepared table to an .rda file.

Usage

download_tcga_rnaseq(
  dataset.name,
  raw.data.dir = "GDCdata/",
  rda.dir = "data/"
)

Arguments

dataset.name

TCGA project id, e.g. "TCGA-LAML".

raw.data.dir

Directory for the raw GDC download.

rda.dir

Directory to save the prepared .rda into.

Value

The prepared expression table from TCGAbiolinks::GDCprepare().

Examples

if (FALSE) { # \dontrun{
download_tcga_rnaseq("TCGA-LAML")
} # }