R/genoprobs2selfprobs.R

In rNeighborQTL: Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

#' Calculating a set of self QTL effects from conditional genotype probabilities
#'
#' A function to reshape \code{qtl}'s object of conditional genotype probabilities, and to calculate self QTL effects for all individuals with given deviation coefficients and conditional genotype probabilities.
#' @param genoprobs Conditional genotype probabilities as taken from \code{qtl::calc.genoprob()}.
#' @param a1 A numeric scalar indicating additive deviation.
#' @param d1 A numeric scalar indicating dominance deviation.
#' @param contrasts A vector composed of three TRUE/FALSE values, which represents the presence/absence of specific genotypes as c(TRUE/FALSE, TRUE/FALSE, TRUE/FALSE) = AA, AB, BB.
#' @return A numeric matrix containing individuals x marker elements for self QTL effects.
#' @author Yasuhiro Sato (\email{sato.yasuhiro.36c@kyoto-u.jp})
genoprobs2selfprobs = function(genoprobs, a1, d1, contrasts=NULL) {
  if (inherits(genoprobs, "cross")) {
    geno <- decompose_genoprobs(genoprobs=genoprobs, contrasts=contrasts)
  } else {
    geno <- genoprobs
  }
  p <- dim(geno$AA)[1]

  selfList <- selfprob(1L:p, a1=a1, d1=d1, AA=geno$AA, AB=geno$AB, BB=geno$BB)

  colnames(selfList) <- rownames(attr(geno,"marker_info"))
  attr(selfList, "contrasts") <- attr(geno, "contrasts")
  return(selfList)
}