TCGA_Download_GeneExpression: The TCGA_Download_GeneExpression function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The TCGA_Download_GeneExpression function

Description

Download gene expression data from TCGA.

Usage

TCGA_Download_GeneExpression(
  CancerSite,
  TargetDirectory,
  mode = "Regular",
  downloadData = TRUE
)

Arguments

CancerSite	character string indicating the TCGA cancer code.
TargetDirectory	character with directory where a folder for downloaded files will be created.
mode	character string indicating whether we should download the gene expression data for miRNAs or lncRNAs, instead of for protein-coding genes. See details for more information.
downloadData	logical indicating if the data should be downloaded (default: TRUE). If False, the url of the desired data is returned.

Details

mode: when mode is set to 'Regular', this function downloads the level 3 RNAseq data (file tag 'mRNAseq_Preprocess.Level_3'). Since there is not enough RNAseq data for OV and GBM, the micro array data is downloaded. If you plan to run the EpiMix on miRNA- or lncRNA-coding genes, please specify the 'mode' parameter to 'miRNA' or 'lncRNA'.

Value

list with paths to downloaded files for gene expression.

Examples

# Example #1 : download regular gene expression data for ovarian cancer
GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV', TargetDirectory = tempdir())

# Example #2 : download miRNA expression data for ovarian cancer
GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV',
                                              TargetDirectory = tempdir(),
                                              mode = 'miRNA')

# Example #3 : download lncRNA expression data for ovarian cancer
GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV',
                                               TargetDirectory = tempdir(),
                                               mode = 'lncRNA')

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.