classifyMut: classifyMut

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

Description

classifyMut

Usage

classifyMut(maf, patient.id = NULL, class = "SP", classByTumor = FALSE, ...)

Arguments

maf	Maf or MafList object generated by readMaf function. Classify SSNVs/Indels into Shared/P-shared/Private, Clonal/Subclonl or Shared-Clonal/P-shared-Clonal/Private-Clonal/Shared-Subclonal/P-shared-SubClonal/Private-SubClonal
patient.id	Select the specific patients. Default NULL, all patients are included
class	The class which would be represented. Default: "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS".
classByTumor	Logical (Default: FALSE). Classify mutations based on "Tumor_ID".
...	Other options passed to subMaf

Value

A data.frame with classification of mutations for each patient

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")
classifyMut(maf, class = "SP")

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