toMesKit: toMeskit

In likelet/CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

toMeskit

Description

Transform a CaMutQC maf object to a MesKit maf object.

Usage

toMesKit(
  maf,
  clinicalFile,
  ccfFile = NULL,
  nonSyn.vc = NULL,
  use.indel.ccf = FALSE,
  ccf.conf.level = 0.95
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
clinicalFile	A clinical data file includes Tumor_Sample_Barcode, Tumor_ID, Patient_ID. Tumor_Sample_Label is optional.
ccfFile	A CCF file of somatic mutations. Default NULL.
nonSyn.vc	List of Variant classifications which are considered as non-silent. Default NULL.
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.

Value

An maf object that can be recognized by MesKit.

Examples

maf_CaMutQC <- vcfToMAF(system.file("extdata/Multi-caller/",
package="CaMutQC"), multiVCF=TRUE)
clin_file <- system.file("extdata", "clin.txt", package="CaMutQC")
maf_MesKit <- toMesKit(maf_CaMutQC, clinicalFile=clin_file)

likelet/CaMutQC documentation built on April 3, 2024, 9:06 a.m.