View source: R/getMAFDataTCGA.R
getMAFdataTCGA | R Documentation |
This function download and extract the mutation data in MAF format from TCGA.
getMAFdataTCGA( cancerCodes = c("ACC"), outputFolder = tempdir(), variant_caller = "mutect2" )
cancerCodes |
A character vector of TCGA cancer codes |
outputFolder |
path of the file containing the mutation information in the MAF format |
variant_caller |
type of variant caller in TCGA |
A vector containing the path of the downloaded mutation annotation files
Mayank Tandon, Ashish Jain
library(MAFDash) cancerCodes <- c("ACC","THCA") outputFolderPath <- tempdir() #maf <- getMAFdataTCGA(cancerCodes = cancerCodes,outputFolder = outputFolderPath)
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