Download_DNAmethylation {MethylMix} | R Documentation |
Downloads DNA methylation data from TCGA.
Download_DNAmethylation(CancerSite, TargetDirectory, downloadData = TRUE)
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. |
list with paths to downloaded files for both 27k and 450k methylation data.
## 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)