R/readCNAProfile.R

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

#' Read CNA Profiles
#'
#' We used a `CNAqc` object, containing a set of mutations, CNA calls and tumor purity values.
#' The CNAqc was used to deal with the allele-specific CNAs.
#'
#' @details
#' This code reads the CNA Profiles for each patient.
#' The tumor names of  maf and seg are required to match each other.
#'
#' @param Patient_ID Patient_ID: select the specific patients.
#' IF not indicate, the input is Maf and seg, or the input is MafList and segList.
#' @param maf Maf or MafList object generated by `readMaf()` function
#' @param seg seg or seglist.
#' @param purity purity information for each samples.
#' @param ref human reference genome version. Default 'hg19'. Optional: 'hg18' or 'hg38'.
#' @return cnaqc.list for cnaqc initiation.
#'
#' @export

readCNAProfile <- function(maf,
                           seg,
                           Patient_ID = NULL,
                           purity = 1,
                           ref = "hg19") {
  if (!is.null(Patient_ID)) {
    maf <- maf[[Patient_ID]]
    seg <- seg[[Patient_ID]]
  }

  # read mutations.
  snvs <- maf@data %>%
    dplyr::mutate(DP = Ref_allele_depth + Alt_allele_depth) %>%
    dplyr::rename(
      chr = Chromosome, from = Start_Position, to = End_Position,
      ref = Reference_Allele,
      alt = Tumor_Seq_Allele2,
      NV = Alt_allele_depth
    ) %>%
    dplyr::select(chr, from, to, ref, alt, DP, NV, VAF, dplyr::everything())

  # read CNAs.
  cna <- seg %>%
    dplyr::rename(
      chr = Chromosome,
      from = Start_Position,
      to = End_Position,
      Major = Major_CN,
      minor = Minor_CN
    ) %>%
    dplyr::select(chr, from, to, Major, minor, dplyr::everything())

  if (!identical(
    unique(sort(snvs$Tumor_Sample_Label)),
    unique(sort(cna$Tumor_Sample_Label))
    # TODO
    # What if snv has more samples or cnv has more samples?
    # a filter operation before asserting is a better option.
  )) {
    stop("The Tumor_Sample_Labels of SNV and CNA are not identical")
  }

  TumorSamples <- unique(sort(snvs$Tumor_Sample_Label))
  cnaqc.list <- list()

  # Get purity info
  if (is.null(names(purity))) {
    # TODO what if each sample has different purity values?
    purity <- setNames(
      rep(purity, length(TumorSamples)),
      nm = TumorSamples
    )
  }

  # TODO how to make sure each purity correctly match to corresponding
  # sample if the samples have different purity values?
  for (i in TumorSamples) {
    cnaqc.list[[i]] <- CNAqc::init(
      snvs %>% dplyr::filter(Tumor_Sample_Label == i),
      cna %>% dplyr::filter(Tumor_Sample_Label == i),
      purity[i],
      ref = ref
    )
  }

  return(cnaqc.list)
}