R/toMesKit.R

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.
#'
#' @param maf An MAF data frame, generated by \code{\link{vcfToMAF}} function.
#' @param clinicalFile A clinical data file includes Tumor_Sample_Barcode, 
#' Tumor_ID, Patient_ID. Tumor_Sample_Label is optional.
#' @param ccfFile A CCF file of somatic mutations. Default NULL.
#' @param nonSyn.vc List of Variant classifications 
#' which are considered as non-silent. Default NULL.
#' @param use.indel.ccf Whether include indels in ccfFile. Default FALSE.
#' @param 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.
#' 
#' @return An maf object that can be recognized by MesKit.
#' @importFrom MesKit readMaf
#' @importFrom methods is
#' @export toMesKit
#' @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)

toMesKit <- function(maf, clinicalFile, ccfFile = NULL, nonSyn.vc = NULL,
                     use.indel.ccf = FALSE, ccf.conf.level = 0.95){
    # check user input
    if (!(is(maf, "data.frame"))) {
      stop("maf input should be a data frame, did you get it from vcfToMAF function?")
    }
    # check whether the input maf is a multisample maf
    if (length(unique(maf$Tumor_Sample_Barcode)) <= 1 ) {
      stop("MesKit is for multi-region data, this maf only contains 1 sample.")
    }
    message("Transforming to MesKit maf...")
    # change refbuild
    refBuild <- switch(unique(maf$NCBI_Build), "GRCh37"="hg19", "GRCh38"="hg38")
    # change certain column names of maf so they can be recognized by MesKit
    colnames(maf)[which(colnames(maf) == "t_ref_count")] <- "Ref_allele_depth"
    colnames(maf)[which(colnames(maf) == "t_alt_count")] <- "Alt_allele_depth"
    
    # write to a temporary file and read it using MesKit immediately
    write.table(maf, "./tmp_maf_for_MesKit.maf", sep="\t", 
                quote=FALSE, row.names=FALSE)
    mafFinal <- MesKit::readMaf(mafFile="./tmp_maf_for_MesKit.maf",
                        clinicalFile=clinicalFile, ccfFile=ccfFile,
                         nonSyn.vc=nonSyn.vc, use.indel.ccf=use.indel.ccf,
                        ccf.conf.level=ccf.conf.level, refBuild=refBuild)
    # remove temporary file immediately
    unlink("./tmp_maf_for_MesKit.maf", recursive=FALSE, force=FALSE)
    # return MesKit object maf
    return(mafFinal)
}