mutCluster: mutCluster

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

Description

Cluster mutations based on variant allele frequencies (VAFs) or cancer cell fractions (CCFs).

Usage

mutCluster(
  maf,
  patient.id = NULL,
  use.ccf = FALSE,
  segFile = NULL,
  withinTumor = FALSE,
  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.
use.ccf	Cluster CCF. Default FALSE.
segFile	The segment file.
withinTumor	Cluster Tumor average CCF within tumors in each patients. Default FALSE.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.
...	Other options passed to subMaf

Value

clustering plots of vaf

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")
mutCluster(maf, patient.id = 'V402')

Niinleslie/MesKit documentation built on Jan. 29, 2022, 10:24 a.m.