readMaf: readMaf

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

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")

MesKit documentation built on March 28, 2021, 6 p.m.