mathScore {MesKit} | R Documentation |
calculates MATH score of each tumor sample or based on Mutant-Allele Tumor Heterogeneity (MATH) approach.
mathScore( maf, patient.id = NULL, withinTumor = FALSE, min.vaf = 0, use.adjVAF = FALSE, segFile = NULL, use.tumorSampleLabel = FALSE, ... )
maf |
Maf or MafList object generated by |
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 |
A data.frame of MATH scores
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.
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)