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.
'#
#' Derive haplotypes of selected individuals
#'
#' Function to devide haplotypes of selected individuals
#' @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 chromosomen Beschraenkung der Haplotypen auf bestimmte Chromosomen (default: 1)
#' @param export.alleles If TRUE export underlying alleles instead of just 012
#' @param non.genotyped.as.missing Set to TRUE to replace non-genotyped markers with NA
#' @param use.id Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: FALSE)
#' @examples
#' data(ex_pop)
#' haplo <- get.haplo(ex_pop, gen=2)
#' @return Haplotype data for in gen/database/cohorts selected individuals
#' @export
get.haplo<- function(population, database=NULL, gen=NULL, cohorts= NULL, chromosomen="all", export.alleles=FALSE,
non.genotyped.as.missing=FALSE, use.id=FALSE){
if(length(chromosomen)==1 && chromosomen=="all"){
subsetting <- FALSE
chromosomen <- 1:length(population$info$snp)
} else{
subsetting <- TRUE
}
if(population$info$miraculix){
if (requireNamespace("miraculix", quietly = TRUE)) {
codeOriginsU <- miraculix::codeOrigins
decodeOriginsU <- miraculix::decodeOrigins
} else{
codeOriginsU <- codeOriginsR
decodeOriginsU <- decodeOriginsR
}
} else{
codeOriginsU <- codeOriginsR
decodeOriginsU <- decodeOriginsR
}
if(length(population$info$origin.gen)>0){
population$info$origin.gen <- as.integer(population$info$origin.gen)
} else{
if(population$info$miraculix){
population$info$origin.gen <- 1:64L
} else{
population$info$origin.gen <- 1:32L
}
}
database <- get.database(population, gen, database, cohorts)
start.chromo <- cumsum(c(1,population$info$snp)[-(length(population$info$snp)+1)])
end.chromo <- population$info$cumsnp
relevant.snps <- NULL
for(index in chromosomen){
relevant.snps <- c(relevant.snps, start.chromo[index]:end.chromo[index])
}
nsnp <- length(relevant.snps)
titel <- t(population$info$snp.base[,relevant.snps])
n.animals <- sum(database[,4] - database[,3] +1)
data <- matrix(0L, ncol=n.animals*2, nrow=nsnp)
before <- 0
names <- numeric(n.animals)
colnames(titel) <- c("Major_Allel", "Minor_Allel")
for(row in 1:nrow(database)){
animals <- database[row,]
nanimals <- database[row,4] - database[row,3] +1
if(nanimals>0){
if(population$info$miraculix && FALSE){
if(subsetting){
data[, (before+1):(before+nanimals*2)] <- miraculix::computeSNPS(population,rep(animals[1], nanimals), rep(animals[2], nanimals) ,animals[3]:animals[4], what="haplo")[relevant.snps,]
} else{
data[, (before+1):(before+nanimals*2)] <- miraculix::computeSNPS(population,rep(animals[1], nanimals), rep(animals[2], nanimals) ,animals[3]:animals[4], what="haplo")
}
}
names[(before+1):(before+nanimals*2)] <- paste(if(animals[2]==1) "M" else "F", rep(animals[3]:animals[4], each=2), "_", animals[1],"_set", 1:2, sep="")
if(TRUE || !population$info$miraculix){
rindex <- 1
for(index in animals[3]:animals[4]){
if(population$info$miraculix && !subsetting){
data[, before + c(rindex,rindex+1)] <- miraculix::computeSNPS(population,animals[1], animals[2] , index, what="haplo")
} else if(population$info$miraculix){
data[, before + c(rindex,rindex+1)] <- miraculix::computeSNPS(population,animals[1], animals[2] , index, what="haplo")[relevant.snps,]
} else{
data[, before + c(rindex,rindex+1)] <- t(compute.snps(population,animals[1], animals[2],index, decodeOriginsU=decodeOriginsU)[,relevant.snps])
}
rindex <- rindex + 2
}
}
}
before <- before + nanimals*2
}
if(non.genotyped.as.missing){
is_genotyped <- get.genotyped.snp(population, database = database)[relevant.snps,]
if(sum(!is_genotyped)>0){
data[,(1:(ncol(data)/2))*2-1][!is_genotyped] <- NA
data[,(1:(ncol(data)/2))*2][!is_genotyped] <- NA
}
}
if(use.id){
colnames(data) <- get.id(population, database = database)
} else{
colnames(data) <- names
}
rownames(data) <- population$info$snp.name[relevant.snps]
if(export.alleles){
return(list(titel,data))
} else{
return(data)
}
}
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