compareCCF {MesKit}R Documentation

compareCCF

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)

[Package MesKit version 1.3.0 Index]