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

In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

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

Author(s)

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
cancerCodes <- c("ACC","THCA")
outputFolderPath <- tempdir()
#maf <- getMAFdataTCGA(cancerCodes = cancerCodes,outputFolder = outputFolderPath)

MAFDash documentation built on April 1, 2022, 9:05 a.m.