GDCquery_Maf: Retrieve open access maf files from GDC server

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.