mathScore: mathScore

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

calculates MATH score of each tumor sample or based on Mutant-Allele Tumor Heterogeneity (MATH) approach.

Usage

mathScore(
  maf,
  patient.id = NULL,
  withinTumor = FALSE,
  min.vaf = 0,
  use.adjVAF = FALSE,
  segFile = NULL,
  use.tumorSampleLabel = FALSE,
  ...
)

Arguments

maf	Maf or MafList object generated by readMaf function.
patient.id	Select the specific patients. Default NULL, all patients are included.
withinTumor	Calculate between-region heterogeneity within tumor. Default: FALSE.
min.vaf	Specify The minimum VAF to filter variants. Default: 0.
use.adjVAF	Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default: FALSE.
segFile	The segment file.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.
...	Other options passed to subMaf

Value

A data.frame of MATH scores

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

maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
mathScore(maf)

MesKit documentation built on March 28, 2021, 6 p.m.