subMaf {MesKit} | R Documentation

## Subset Maf object

### Description

Subset Maf object

### Usage

    subMaf(
      maf,
      mafObj = FALSE,
      patient.id = NULL,
      geneList = NULL,
      chrSilent = NULL,
      mutType = "All",
      use.indel = TRUE,
      min.vaf = 0,
      max.vaf = 1,
      min.average.vaf = 0,
      min.ccf = 0,
      min.ref.depth = 0,
      min.alt.depth = 0,
      min.total.depth = 0,
      clonalStatus = NULL,
      use.adjVAF = FALSE,
      use.tumorSampleLabel = FALSE
    )

### Arguments

`maf` | Maf or MafList object generated by `readMaf` function.
`mafObj` | return Maf class. (Default: FALSE).
`patient.id` | Select the specific patients. Default NULL, all patients are included.
`geneList` | A list of genes to restrict the analysis. Default NULL.
`chrSilent` | Chromosomes excluded in the analysis. e.g, 1, 2, X, Y. Default NULL.
`mutType` | Select Proper variant classification you need. Default "All". Option: "nonSyn".
`use.indel` | Logical value. Whether to use INDELs besides somatic SNVs. (Default: TRUE).
`min.vaf` | The minimum VAF for filtering variants. Default 0.
`max.vaf` | The maximum VAF for filtering variants. Default 1.
`min.average.vaf` | The minimum tumor average VAF for filtering variants. Default 0.
`min.ccf` | The minimum CCF for filtering variants. Default NULL.
`min.ref.depth` | The minimum reference allele depth for filtering variants. Default 0.
`min.alt.depth` | The minimum alteratation allele depth for filtering variants. Default 0.
`min.total.depth` | The minimum total allele depth for filtering variants. Default 0.
`clonalStatus` | Subset by clonal status. Default NULL. Option: "Clonal","Subclonal".
`use.adjVAF` | Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.
`use.tumorSampleLabel` | Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.

### Value

Maf object or Maf data.

### 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")
    maf_data <- subMaf(maf)

[Package MesKit version 1.4.0 Index]