get_biomarker_from_maf: Produce a Table of Biomarker Values from a MAF

In ICBioMark: Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers

Description

A function to recover true biomarker values from a mutation annotation file.

Usage

get_biomarker_from_maf(
  maf,
  biomarker = "TIB",
  sample_list = NULL,
  gene_list = NULL,
  biomarker_name = NULL
)

Arguments

maf	(dataframe) A table of annotated mutations containing the columns 'Tumor_Sample_Barcode', 'Hugo_Symbol', and 'Variant_Classification'.
biomarker	(character) Which biomarker needs calculating? If "TMB" or "TIB", then appropriate mutation types will be selected. Otherwise, will be interpreted as a vector of characters denoting mutation types to include.
sample_list	(character) Vector of characters giving a list of values of Tumor_Sample_Barcode to include.
gene_list	(character) Vector of characters giving a list of genes to include in calculation of biomarker.
biomarker_name	(character) Name of biomarker. Only needed if biomarker is not "TMB" or "TIB"

Value

A dataframe with two columns, 'Tumor_Sample_Barcode' and values of the biomarker specified.

Examples

print(head(get_biomarker_from_maf(example_maf_data$maf, sample_list = paste0("SAMPLE_", 1:100))))

ICBioMark documentation built on Nov. 15, 2021, 5:09 p.m.