make_mut_matrix: Make mutation matrix using maf data

In IOBR/IOBR: Immune Oncology Biological Research

Make mutation matrix using maf data

Description

Make mutation matrix using maf data

Usage

make_mut_matrix(
  maf = NULL,
  mut_data = NULL,
  isTCGA = TRUE,
  category = "multi",
  Tumor_Sample_Barcode = "Tumor_Sample_Barcode",
  Hugo_Symbol = "Hugo_Symbol",
  Variant_Classification = "Variant_Classification",
  Variant_Type = "Variant_Type"
)

Arguments

maf	file name or a maf object
mut_data	if maf data had beed loaded, this argument will be applied
isTCGA	logical variable,
category	if category is 'multi', four mutation matrix will be generated: all, snp, indel and frameshift
Tumor_Sample_Barcode	column name of tumor sample
Hugo_Symbol	column name of gene symbol
Variant_Classification	column name of variant classification: Frame_Shift_Del
Variant_Type	column name of variant type: SNP, INS, DEL

Author(s)

Dongqian Zeng

Shixiang Huang

Examples

library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-STAD", data.category = "Simple Nucleotide Variation", access = "open", data.type = "Masked Somatic Mutation", workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" )
GDCdownload(query)
maf <- GDCprepare(query)
mut_list <- make_mut_matrix(maf = maf, isTCGA   = T, category = "multi")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.