GDCquery_Maf {TCGAbiolinks} | R Documentation

## Retrieve open access maf files from GDC server

### Description

GDCquery_Maf uses the following guide to download maf files https://gdc-docs.nci.nih.gov/Data/Release_Notes/Data_Release_Notes/

### Usage

    GDCquery_Maf(tumor, save.csv = FALSE, directory = "GDCdata",
      pipelines = NULL)

### Arguments

`tumor` | a valid tumor
`save.csv` | Write maf file into a csv document
`directory` | Directory/Folder where the data will downloaded. Default: GDCdata
`pipelines` | Four separate variant calling pipelines are implemented for GDC data harmonization. Options: muse, varscan2, somaticsniper, mutect2. For more information: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

### Value

A data frame with the maf file information

### Examples

    ## Not run:
       acc.muse.maf <- GDCquery_Maf("ACC", pipelines = "muse")
       acc.varscan2.maf <- GDCquery_Maf("ACC", pipelines = "varscan2")
       acc.somaticsniper.maf <- GDCquery_Maf("ACC", pipelines = "somaticsniper")
       acc.mutect.maf <- GDCquery_Maf("ACC", pipelines = "mutect2")

    ## End(Not run)

[Package TCGAbiolinks version 2.14.0 Index]