R/mpcross.R

In mpMap: Multi-parent RIL genetic analysis

#' Multi-parent cross object
#' 
#' The class of object generated from \code{sim.mpcross} and the format input to functions to construct linkage maps for multi-parent crosses. Basic constructor - takes required R objects and formats as an mpcross object.
#' @aliases mpcross.object print.mpcross mpcross
#' @export
#' @param founders Matrix of founder genotypes
#' @param finals Matrix of final genotypes
#' @param pedigree Cross pedigree
#' @param id Vector of numeric IDs for lines (which rows in pedigree are observed)
#' @param fid Vector of founder IDs
#' @return Let n.founders be the number of founders (either 4 or 8); n.finals be the number of final RILs genotyped; and n.mrk be the number of markers genotyped. Then
#' \item{founders}{ Founder genotypes - a matrix with dimensions n.founders x n.mrk. Row names of the matrix should be lines names; Column names should be marker names}
#' \item{finals}{ Final genotypes - a matrix with dimensions n.finals x n.mrk. Row names of the matrix should be line name; column names should be marker names.}
#' \item{id}{ Vector of final IDs with length n.finals}
#' \item{fid}{ Vector of founder IDs with length n.founders}
#' \item{pedigree}{ Numeric pedigree with 3 columns - mother, father, ID}
#' \item{pheno}{ Phenotypic data}

#' Optional components:
#' \item{map}{ Linkage map - either from which data was generated in \code{sim.mpcross} or estimated at some point}
#' \item{ibd}{ IBD genotypes from founders if data has been generated from \code{sim.mpcross}}
#' \item{qtlgeno}{ Genotypes at QTL if data has been generated from \code{sim.mpcross}}
#' \item{rf}{ Recombination fractions if data has been analyzed with \code{mpestrf}}
#' \item{lg}{ Linkage groups if data has been analyzed with \code{mpgroup}}
#' @seealso \code{\link[mpMap]{sim.mpcross}}, \code{\link[mpMap]{mpestrf}}, \code{\link[mpMap]{mpgroup}}
#' @examples
#' map <- sim.map(len=rep(100,2), n.mar=11, eq.spacing=TRUE, include.x=FALSE)
#' sim.ped <- sim.mpped(4, 1, 500, 6, 1)
#' sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)

mpcross <- function(founders, finals, pedigree, id, fid)
{
  ## constructor function
  object <- list()
  object$founders <- founders
  object$finals <- finals
  object$pedigree <- pedigree
  object$id <- id
  object$fid <- fid

  class(object) <- "mpcross"
  attr(object, "type") <- paste("ri", nrow(founders), "self", sep="")
  object
}