R/geno2Cross.R

In MPR.genotyping: Maximum Parsimony of Recombination to Infer Parental Genotypes

geno2Cross <-
function (geno.data, pheno.data, cm_unit = 250000) 
  {
    myGeno.data <- geno.data
    geno.value <- sort(unique(na.omit(c(myGeno.data))))
    if (identical(as.numeric(geno.value), c(0, 1))) {
      myGeno.data <- myGeno.data + 1
      geno.value <- sort(unique(na.omit(c(myGeno.data))))
    }
    if (!identical(as.numeric(geno.value), c(1, 2))) 
      stop("the value of geno.data should be 1, 2, or NA.")
    ids.RILs <- match(colnames(myGeno.data), rownames(pheno.data))
    myGeno.site <- data.frame(Chr = as.numeric(substr(rownames(myGeno.data), 
                                                      1, 2)), Position = as.numeric(substr(rownames(myGeno.data), 
                                                                                           3, 10)))
    myCrossData <- list()
    myCrossData$geno <- lapply(split(1:nrow(myGeno.data), myGeno.site$Chr), 
                               function(ids) {
                                 myMarkers <- myGeno.site$Position[ids]/cm_unit
                                 names(myMarkers) <- rownames(myGeno.data)[ids]
                                 myMap <- list(data = t(myGeno.data[ids, ]), map = myMarkers)
                                 class(myMap) <- "A"
                                 myMap
                               })
    myCrossData$pheno <- as.data.frame(pheno.data[ids.RILs, ])
    class(myCrossData) <- c("riself", "cross")
    attr(myCrossData, "alleles") <- c("A", "B")
    myCrossData
  }