R/get.genotyped.R

In MoBPS: Modular Breeding Program Simulator

'#
  Authors
Torsten Pook, torsten.pook@wur.nl

Copyright (C) 2017 -- 2025  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.
'#

#' Derive genotyping status
#'
#' Function to if selected individuals are genotyped
#' @param population Population list
#' @param database Groups of individuals to consider for the export
#' @param gen Quick-insert for database (vector of all generations to export)
#' @param cohorts Quick-insert for database (vector of names of cohorts to export)
#' @param id Individual IDs to search/collect in the database
#' @param use.id Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)
#' @param use.all.copy Set to TRUE to extract phenotyping
#' @examples
#' data(ex_pop)
#' get.genotyped(ex_pop, gen=2)
#' @return Check if in gen/database/cohorts selected individuals are genotyped
#' @export

get.genotyped <- function(population, database=NULL, gen=NULL, cohorts=NULL, id = NULL, use.id=TRUE,
                          use.all.copy = FALSE){

  database <- get.database(population, gen, database, cohorts, id = id)
  n.animals <- sum(database[,4] - database[,3] +1)
  genotyped <- colnamed <- numeric(n.animals)
  rindex <- 1

  if(use.all.copy){

    for(row in 1:nrow(database)){
      animals <- database[row,]
      if(diff(database[row,3:4])>(-1)){
        for(index in database[row,3]:database[row,4]){
          colnamed[rindex] <- paste(if(animals[2]==1) "M" else "F", index,"_", animals[1],sep="")
          copies <- population$breeding[[animals[1]]][[animals[2]]][[index]][[21]]
          for(rows in 1:nrow(copies)){
            if(population$breeding[[copies[rows,1]]][[copies[rows,2]]][[copies[rows,3]]][[16]]==1){
              genotyped[rindex] <- 1
            }
          }
          rindex <- rindex + 1
        }
      }

    }



  } else{
    for(row in 1:nrow(database)){
      animals <- database[row,]
      if(diff(database[row,3:4])>(-1)){
        for(index in database[row,3]:database[row,4]){
          genotyped[rindex] <- population$breeding[[database[row,1]]][[database[row,2]]][[index]][[16]]
          colnamed[rindex] <- paste(if(animals[2]==1) "M" else "F", index,"_", animals[1],sep="")
          rindex <- rindex + 1
        }
      }

    }
  }



  if(use.id){
    names(genotyped) <- get.id(population, database = database)
  } else{
    names(genotyped) <- colnamed
  }

  genotyped <- genotyped>0
  return(genotyped)
}