Download_DNAmethylation: The Download_DNAmethylation function

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

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)
 

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