R/write_map.R

In onemap: Construction of Genetic Maps in Experimental Crosses

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# Package: onemap                                                     #
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# File: write_map.R                                                   #
# Contains: write_map                                                 #
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# Written by Marcelo Mollinari                                        #
# copyright (c) 2010, Marcelo Mollinari                               #
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# First version: 10/10/2010                                           #
# License: GNU General Public License version 2 (June, 1991) or later #
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##' Write a genetic map to a file
##'
##' Write a genetic map to a file, base on a given map, or a list of maps. The
##' output file can be used as an input to perform QTL mapping using the package
##' R/qtl. It is also possible to create an output to be used with
##' QTLCartographer program.
##'
##' This function is available only for backcross, F2 and RILs.
##'
##' @param map.list a map, i.e. an object of class \code{sequence} with a
##' predefined order, linkage phases, recombination fraction and likelihood or
##' a list of maps.
##' @param file.out output map file.
##' @author Marcelo Mollinari, \email{mmollina@@usp.br}
##' @references Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B.
##' (2008) \emph{qtl: Tools for analyzing QTL experiments} R package version
##' 1.09-43
##' 
##' @return file with genetic map information
##'
##' Wang S., Basten, C. J. and Zeng Z.-B. (2010) Windows QTL Cartographer 2.5.
##' Department of Statistics, North Carolina State University, Raleigh, NC.
##' @keywords rqtl
##' @examples
##' \donttest{
##' data(mapmaker_example_f2)
##' twopt<-rf_2pts(mapmaker_example_f2)
##' lg<-group(make_seq(twopt, "all"))
##' 
##' ##"pre-allocate" an empty list of length lg$n.groups (3, in this case)
##' maps.list<-vector("list", lg$n.groups)
##' 
##' for(i in 1:lg$n.groups){
##'   ##create linkage group i
##'   LG.cur <- make_seq(lg,i)
##'   ##ordering
##'   map.cur<-order_seq(LG.cur, subset.search = "sample")
##'   ##assign the map of the i-th group to the maps.list
##'   maps.list[[i]]<-make_seq(map.cur, "force")
##' 
##'   ##write maps.list to ".map" file
##'   write_map(maps.list, tempfile(fileext = ".map"))
##' 
##' }
##' }
##' 
##'@export
write_map<-function(map.list,file.out){
   # checking for correct object
  if(!(inherits(map.list,"list") | inherits(map.list,"sequence"))) stop(deparse(substitute(map.list))," is not an object of class 'list' or 'sequnece'")
  if(!inherits(file.out,"character")) stop(deparse(substitute(file.out))," is an invalid output file name")

  # if map.list is just a single chormosome, convert it  into a list
  if(inherits(map.list,"sequence")) map.list<-list(map.list)

  write(x="",file=file.out)
  for(i in 1:length(map.list)){
    if(!inherits(map.list[[i]],"sequence")) stop("Object ", i , " in map.list is not an object of class 'sequence'")
    if(is.null(map.list[[i]]$seq.like))  stop("Parameters are not estimated for object ", i, " in map.list")
    map<-cumsum(c(0,get(get(".map.fun", envir=.onemapEnv))(map.list[[i]]$seq.rf)))
    marnames<-colnames(map.list[[i]]$data.name$geno)[map.list[[i]]$seq.num]
    write(t(cbind(i,marnames,map)), file=file.out, ncolumns =3, append=TRUE)
  }
}