math.score: calculates MATH (Mutant-Allele Tumor Heterogeneity) score.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

calcuates MATH scores from variant allele frequencies. Mutant-Allele Tumor Heterogeneity (MATH) score is a measure of intra-tumor genetic heterogeneity. High MATH scores are related to lower survival rates. This function requies vafs.

Usage

math.score(maf, vafCol = NULL, sampleName = NULL, vafCutOff = 0.075)

Arguments

maf	an MAF object generated by read.maf
vafCol	manually specify column name for vafs. Default looks for column 't_vaf'
sampleName	sample name for which MATH score to be calculated. If NULL, calculates for all samples.
vafCutOff	minimum vaf for a variant to be considered for score calculation. Default 0.075

Value

data.table with MATH score for every Tumor_Sample_Barcode

References

Mroz, Edmund A. et al. Intra-Tumor Genetic Heterogeneity and Mortality in Head and Neck Cancer: Analysis of Data from The Cancer Genome Atlas. Ed. Andrew H. Beck. PLoS Medicine 12.2 (2015): e1001786.

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.math <- math.score(maf = laml, vafCol = 'i_TumorVAF_WU',
sampleName = c('TCGA-AB-3009', 'TCGA-AB-2849', 'TCGA-AB-3002', 'TCGA-AB-2972'))

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.545s elapsed (0.454s cpu) 

maftools documentation built on Feb. 6, 2021, 2 a.m.