Download_GeneExpression {MethylMix} | R Documentation

## The Download_GeneExpression function

### 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)

[Package MethylMix version 2.24.0 Index]