make_mut_matrix: Construct Mutation Matrices from MAF Data

In IOBR: Immune Oncology Biological Research

Construct Mutation Matrices from MAF Data

Description

Builds mutation presence/absence matrices from MAF input (file path or MAF object). Supports multiple categories: all mutations, SNPs, indels, and frameshift mutations. When category = "multi", returns a list of matrices for each category. Compatible with TCGA-formatted data.

Usage

make_mut_matrix(
  maf = NULL,
  mut_data = NULL,
  isTCGA = TRUE,
  category = c("multi", "all", "snp", "indel", "frameshift"),
  Tumor_Sample_Barcode = "Tumor_Sample_Barcode",
  Hugo_Symbol = "Hugo_Symbol",
  Variant_Classification = "Variant_Classification",
  Variant_Type = "Variant_Type"
)

Arguments

maf	Character or MAF object. Path to MAF file or an already loaded MAF object.
mut_data	Data frame or NULL. Preloaded MAF-like data (used if 'maf' is NULL).
isTCGA	Logical. Whether the MAF follows TCGA conventions. Default is TRUE.
category	Character. Mutation category: "all", "snp", "indel", "frameshift", or "multi". Default is "multi".
Tumor_Sample_Barcode	Character. Column name for tumor sample IDs. Default is "Tumor_Sample_Barcode".
Hugo_Symbol	Character. Column name for gene symbols. Default is "Hugo_Symbol".
Variant_Classification	Character. Column name for variant classification (e.g., Frame_Shift_Del). Default is "Variant_Classification".
Variant_Type	Character. Column name for variant type (e.g., SNP, INS, DEL). Default is "Variant_Type".

Value

List of mutation matrices (if category = "multi") or a single matrix for the specified category.

Note

Some users may encounter errors from upstream data import (e.g. "Can't combine ..$Tumor_Seq_Allele2" when using TCGAbiolinks or TCGAmutations). This is due to inconsistent column types in the source MAF tables, not an issue of this function. Please ensure your MAF or merged data frame uses consistent column types (e.g. convert allele columns to character before input).

Author(s)

Dongqian Zeng

Shixiang Huang

Examples

## Not run: 
# See maftools or TCGAbiolinks documentation for obtaining MAF input
# Example: Download MAF file from TCGA portal
mut_list <- make_mut_matrix(maf = "path_to_maf_file.maf", isTCGA = TRUE, category = "multi")

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.