classifyMut {MesKit} | R Documentation

## classifyMut

### Description

classifyMut

### Usage

    classifyMut(maf, patient.id = NULL, class = "SP", classByTumor = FALSE, ...)

### Arguments

`maf` | Maf or MafList object generated by `readMaf` function. Classify SSNVs/Indels into Shared/P-shared/Private, Clonal/Subclonl or Shared-Clonal/P-shared-Clonal/Private-Clonal/Shared-Subclonal/P-shared-SubClonal/Private-SubClonal
`patient.id` | Select the specific patients. Default NULL, all patients are included
`class` | The class which would be represented. Default: "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS".
`classByTumor` | Logical (Default: FALSE). Classify mutations based on "Tumor_ID".
`...` | Other options passed to `subMaf`

### Value

A data.frame with classification of mutations for each patient

### 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")
    classifyMut(maf, class = "SP")

[Package MesKit version 1.4.0 Index]