mutCluster {MesKit} | R Documentation

## mutCluster

### 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')

[Package MesKit version 1.4.0 Index]