Download_GeneExpression {MethylMix} | R Documentation |
Downloads gene expression data from TCGA.
Download_GeneExpression(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. |
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
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) # 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)