maftools (version 0.99.30)

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

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, plotFile = NULL, vafCol = NULL, sampleName = NULL,
  vafCutOff = 0.075)

Arguments

maf

an MAF object generated by read.maf

plotFile

file name for output plot.

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

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
laml.math <- math.score(maf = laml, vafCol = 'i_TumorVAF_WU',
sampleName = c('TCGA.AB.3009', 'TCGA.AB.2849', 'TCGA.AB.3002', 'TCGA.AB.2972'))
# }