compareCCF: compareCCF

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

Description

Compare the CCF between samples/tumor pairs This function requires CCF for clustering

Usage

compareCCF(
  maf,
  patient.id = NULL,
  min.ccf = 0,
  pairByTumor = 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.
min.ccf	The minimum value of CCF. Default 0.
pairByTumor	Pair by tumor types 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

a result list of CCF comparing between samples/tumor pairs

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")
compareCCF(maf)

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