math.score {maftools} | R Documentation

## 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, 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'))

[Package maftools version 2.10.05 Index]