Download_GeneExpression: The Download_GeneExpression function

In gevaertlab/methylmix: MethylMix: Identifying methylation driven cancer genes

Description

Downloads gene expression data from TCGA.

Usage

Download_GeneExpression(CancerSite, TargetDirectory, downloadData = TRUE)

Arguments

CancerSite	character of length 1 with TCGA cancer code.
TargetDirectory	character with directory where a folder for downloaded files will be created.
downloadData	logical indicating if data should be downloaded (default: TRUE). If false, the url of the desired data is returned.

Details

This function downloads RNAseq data (file tag "mRNAseq_Preprocess.Level_3"), with the exception for OV and GBM, for which micro array data is downloaded since there is not enough RNAseq data

Value

list with paths to downloaded files for both 27k and 450k methylation data.

Examples

## Not run: 

# Optional register cluster to run in parallel
library(doParallel)
cl <- makeCluster(5)
registerDoParallel(cl)

# Gene expression data for ovarian cancer
cancerSite <- "OV"
targetDirectory <- paste0(getwd(), "/")

# Downloading gene expression data
GEdirectories <- Download_GeneExpression(cancerSite, targetDirectory, TRUE)

# Processing gene expression data
GEProcessedData <- Preprocess_GeneExpression(cancerSite, GEdirectories)

# Saving gene expression processed data
saveRDS(GEProcessedData, file = paste0(targetDirectory, "GE_", cancerSite, "_Processed.rds"))

stopCluster(cl)

## End(Not run)

gevaertlab/methylmix documentation built on May 25, 2019, 5:25 p.m.