MAFDash (version 0.2.1)

getMAFdataTCGA: Function to extract the mutation data in MAF format from TCGA

Description

This function download and extract the mutation data in MAF format from TCGA.

Usage

getMAFdataTCGA(
  cancerCodes = c("ACC"),
  outputFolder = tempdir(),
  variant_caller = "mutect2"
)

Arguments

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

Value

A vector containing the path of the downloaded mutation annotation files

Examples

# NOT RUN {
library(MAFDash)
cancerCodes <- c("ACC","THCA")
outputFolderPath <- tempdir()
#maf <- getMAFdataTCGA(cancerCodes = cancerCodes,outputFolder = outputFolderPath)
# }