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 1.4.0 Index]