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).