R/genotypeToCharacter.R

In GWASTools: Tools for Genome Wide Association Studies

pasteSorted <- function(a, b, sep="/") {
    paste(pmin(a,b), pmax(a,b), sep=sep)
}


genotypeToCharacter <- function(geno, alleleA=NULL, alleleB=NULL, sort=TRUE) {
  if (is.null(alleleA) | is.null(alleleB)) {
    geno[geno %in% 0] <- "B/B"
    geno[geno %in% 1] <- "A/B"
    geno[geno %in% 2] <- "A/A"
  } else {

    stopifnot(length(alleleA) == length(alleleB))

    geno.is.vec <- length(dim(geno)) < 2
    allele.single.char <- length(alleleA) == 1
    if (geno.is.vec & !allele.single.char) stopifnot(length(geno) == length(alleleA))
    if (!geno.is.vec & !allele.single.char) stopifnot(nrow(geno) == length(alleleA))
    if (!geno.is.vec & allele.single.char) stopifnot(nrow(geno) == length(alleleA))

    alleleA <- as.character(alleleA)
    alleleB <- as.character(alleleB)
    aa <- paste(alleleA, alleleA, sep="/")
    bb <- paste(alleleB, alleleB, sep="/")
    if (sort) {
      ab <- pasteSorted(alleleA, alleleB, sep="/")
    } else {
      ab <- paste(alleleA, alleleB, sep="/")
    }
    ## if alleles are NA, genotype should be missing
    aa[is.na(alleleA)] <- NA
    bb[is.na(alleleB)] <- NA
    ab[is.na(alleleA) | is.na(alleleB)] <- NA

    if (geno.is.vec & allele.single.char) {
      geno[geno %in% 0] <- bb
      geno[geno %in% 1] <- ab
      geno[geno %in% 2] <- aa
    } else {
      if (geno.is.vec) {
        geno <- matrix(geno, ncol=1)
      }
      for (k in 1:ncol(geno)) {
        geno[geno[,k] %in% 0, k] <- bb[geno[,k] %in% 0]
        geno[geno[,k] %in% 1, k] <- ab[geno[,k] %in% 1]
        geno[geno[,k] %in% 2, k] <- aa[geno[,k] %in% 2]
      }
      if (ncol(geno) == 1) {
        geno <- as.vector(geno)
      }
    }
  }
  return(geno)
}