Nothing
'#
Authors
Torsten Pook, torsten.pook@uni-goettingen.de
Copyright (C) 2017 -- 2020 Torsten Pook
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
'#
#' Map generation
#'
#' Function to derive the genomic map for a given population list
#' @param population Population list
#' @param use.snp.nr Set to TRUE to display SNP number and not SNP name
#' @examples
#' data(ex_pop)
#' map <- get.map(ex_pop)
#' @return Genomic map of the population list
#' @export
get.map <- function(population, use.snp.nr=FALSE){
chr.nr <- snp.nr <- numeric(sum(population$info$snp))
start <- 1
for(index in 1:length(population$info$snp)){
if(population$info$snp[index]>0){
chr.nr[start:(start+population$info$snp[index]-1)] <- index
snp.nr[start:(start+population$info$snp[index]-1)] <- 1:population$info$snp[index]
start <- start + population$info$snp[index]
}
}
if(use.snp.nr){
mapfile <- cbind(chr.nr, snp.nr, 0 , as.numeric(population$info$bp))
} else{
mapfile <- cbind(chr.nr, population$info$snp.name, 0 , as.numeric(population$info$bp))
}
mapfile[is.na(mapfile)] <- 0
return(mapfile)
}
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