Download_DNAmethylation {MethylMix} | R Documentation

## The Download_DNAmethylation function

### Description

Downloads DNA methylation data from TCGA.

### Usage

    Download_DNAmethylation(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.

### 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)

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

    # Downloading methylation data
    METdirectories <- Download_DNAmethylation(cancerSite, targetDirectory, TRUE)

    # Processing methylation data
    METProcessedData <- Preprocess_DNAmethylation(cancerSite, METdirectories)

    # Saving methylation processed data
    saveRDS(METProcessedData, file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds"))

    # Clustering methylation data
    res <- ClusterProbes(METProcessedData[[1]], METProcessedData[[2]])

    # Saving methylation clustered data
    toSave <- list(METcancer = res[[1]], METnormal = res[[2]], ProbeMapping = res$ProbeMapping)
    saveRDS(toSave, file = paste0(targetDirectory, "MET_", cancerSite, "_Clustered.rds"))

    stopCluster(cl)

    ## End(Not run)

[Package MethylMix version 2.10.2 Index]