R/cross2gpData.r

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

cross2gpData <- function(cross) {
  # check for class
  # sometimes multiple classes in package 'qtl'
  if (all(class(cross) != "cross")) stop("object '", substitute(cross), "' not of class 'cross'")
  # phenotypic data
  pheno <- cross$pheno
  # names of chromosomes
  chr <- names(cross$geno)
  # extract information from first chromosome
  geno <- cross$geno[[chr[1]]]$data
  map <- data.frame(chr = chr[1], pos = cross$geno[[chr[1]]]$map)
  # loop over chromosomes 2:n
  if (length(chr) > 1) {
    for (i in chr[-1]) {
      # add new genotypes
      geno <- cbind(geno, cross$geno[[i]]$data)
      # add new map info
      map <- rbind(map, data.frame(chr = i, pos = cross$geno[[i]]$map))
    }
  }
  # combine pheno, geno, and map  in class 'gpData'
  ret <- create.gpData(pheno = pheno, geno = geno, map = map)
  # recode
  # coding in cross: 1 = AA, 2 = AB, 3 = BB,
  ret$geno <- ret$geno - 1
  return(ret)
}