readMaf {MesKit} | R Documentation

## readMaf

### Description

Read tab delimited MAF (can be plain text or *.gz compressed) file along with sample information file.

### Usage

    readMaf(
      mafFile,
      clinicalFile,
      ccfFile = NULL,
      adjusted.VAF = FALSE,
      nonSyn.vc = NULL,
      use.indel.ccf = FALSE,
      ccf.conf.level = 0.95,
      refBuild = "hg19"
    )

### Arguments

`mafFile` | A tab delimited MAF file (plain text or *.gz compressed). Required.
`clinicalFile` | A clinical data file includes Tumor_Sample_Barcode, Tumor_ID, Patient_ID. Tumor_Sample_Label is optional. Default NULL.
`ccfFile` | A CCF file of somatic mutations. Default NULL.
`adjusted.VAF` | Whether adjusted VAF is included in mafFile. Default FALSE.
`nonSyn.vc` | List of Variant classifications which are considered as non-silent. Default NULL, use Variant Classifications with "Frame_Shift_Del","Frame_Shift_Ins","Splice_Site","Translation_Start_Site","Nonsense_Mutation","Nonstop_Mutation","In_Frame_Del","In_Frame_Ins","Missense_Mutation"
`use.indel.ccf` | Whether include indels in ccfFile. Default FALSE.
`ccf.conf.level` | The confidence level of CCF to identify clonal or subclonal. Only works when "CCF_std" or "CCF_CI_high" is provided in ccfFile. Default 0.95.
`refBuild` | Human reference genome version. Default 'hg19'. Optional: 'hg18' or 'hg38'.

### Value

an object of Maf or MafList.

### 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, refBuild="hg19")
    maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")

[Package MesKit version 1.4.0 Index]