mutCluster: mutCluster

Description Usage Arguments Value Examples

View source: R/mutCluster.R

Description

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

Usage

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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

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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')

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