R/map_func.R

In onemap: Construction of Genetic Maps in Experimental Crosses

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#                                                                     #
# Package: onemap                                                     #
#                                                                     #
# File: map_func.R                                                    #
# Contains: haldane, kosambi, set_map_fun                             #
#                                                                     #
# Written by Gabriel Rodrigues Alves Margarido and Marcelo Mollinari  #
# copyright (c) 2007-9, Gabriel R A Margarido                         #
#                                                                     #
# First version: 11/07/2007                                           #
# License: GNU General Public License version 2 (June, 1991) or later #
#                                                                     #
#######################################################################

#' Apply Haldane mapping function
#' 
#' @param rcmb vector of recombination fraction values
#' 
#' @return vector with centimorgan values
#' 
#' @export
haldane <- function(rcmb) {
  # rcmb must be a number between 0 and 0.5
  if (is.numeric(rcmb) & !any(is.nan(rcmb))) {
    if (all(rcmb >= 0) & all(rcmb <= 0.5)){
      return(100*-(1/2)*log(1-2*rcmb))  # haldane mapping fuction
    } else {stop("the recombination fraction must be between 0 and 0.5")}
  }
  else stop("the argument to 'haldane' function must be ",
            dQuote("numeric"),". Check if you don't have excess of missing data in your onemap object.")
}

#' Apply Kosambi mapping function
#' 
#' @param rcmb vector of recombination fraction values
#' 
#' @return vector with centimorgan values
#' 
#' @export
kosambi <- function(rcmb) {
  # rcmb must be a number between 0 and 0.5
  if (is.numeric(rcmb) & !any(is.nan(rcmb))) {
    if (all(rcmb >= 0) && all(rcmb <= 0.5)){
      return(100/4*log(abs((1+2*rcmb)/(1-2*rcmb))))  # kosambi mapping fuction
    }else {stop("the recombination fraction must be between 0 and 0.5")}
  }
  else stop("the argument to 'kosambi' function must be ",
            dQuote("numeric"), ". Check if you don't have excess of missing data in your onemap object.")
}



##' Defines the default mapping function
##'
##' Defines the function that should be used to display the genetic map through
##' the analysis.
##'
##'
##' @param type Indicates the function that should be used, which can be
##' \code{"kosambi"} or \code{"haldane"}
##' 
##' @author Marcelo Mollinari, \email{mmollina@@usp.br}
##' @seealso \code{\link[onemap]{kosambi}} and \code{\link[onemap]{haldane}}
##' @references Haldane, J. B. S. (1919) The combination of linkage values and
##' the calculation of distance between the loci of linked factors.
##' \emph{Journal of Genetics} 8: 299-309.
##' 
##' @return No return value, called for side effects
##'
##' Kosambi, D. D. (1944) The estimation of map distance from recombination
##' values. \emph{Annuaire of Eugenetics} 12: 172-175.
##' @keywords arith
##' 
##' @export
set_map_fun<- function(type=c("kosambi", "haldane")){
    type<-match.arg(type,c("kosambi", "haldane"))
    if(type=="haldane") assign(".map.fun",  "haldane", envir = .onemapEnv)
    else assign(".map.fun",  "kosambi", envir = .onemapEnv)
  }

# end of file