Nothing
######################################################################
#
# sim.geno.R
#
# copyright (c) 2001-2019, Karl W Broman
# last modified Dec, 2019
# first written Feb, 2001
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# 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, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: sim.geno
#
######################################################################
######################################################################
#
# sim.geno: simulate from the joint distribution Pr(g | O)
#
######################################################################
sim.geno <-
function(cross, n.draws=16, step=0, off.end=0, error.prob=0.0001,
map.function=c("haldane","kosambi","c-f","morgan"),
stepwidth=c("fixed", "variable", "max"))
{
if(!inherits(cross, "cross"))
stop("Input should have class \"cross\".")
# map function
map.function <- match.arg(map.function)
if(map.function=="kosambi") mf <- mf.k
else if(map.function=="c-f") mf <- mf.cf
else if(map.function=="morgan") mf <- mf.m
else mf <- mf.h
stepwidth <- match.arg(stepwidth)
# don't let error.prob be exactly zero, just in case
if(error.prob < 1e-50) error.prob <- 1e-50
if(error.prob > 1) {
error.prob <- 1-1e-50
warning("error.prob shouldn't be > 1!")
}
n.ind <- nind(cross)
n.chr <- nchr(cross)
n.mar <- nmar(cross)
type <- crosstype(cross)
# calculate genotype probabilities one chromosome at a time
for(i in 1:n.chr) {
if(n.mar[i]==1) temp.offend <- max(c(off.end,5))
else temp.offend <- off.end
chr_type <- chrtype(cross$geno[[i]])
if(chr_type=="X") xchr <- TRUE
else xchr <- FALSE
# which type of cross is this?
if(type == "f2") {
n.gen <- 3
one.map <- TRUE
if(!xchr) # autosomal
cfunc <- "sim_geno_f2"
else # X chromsome
cfunc <- "sim_geno_bc"
}
else if(type == "bc" || type=="riself" || type=="risib" || type=="dh" || type=="haploid") {
cfunc <- "sim_geno_bc"
n.gen <- 2
one.map <- TRUE
}
else if(type == "4way") {
n.gen <- 4
cfunc <- "sim_geno_4way"
one.map <- FALSE
}
else if(type=="ri8sib" || type=="ri4sib" || type=="ri8self" || type=="ri4self" || type=="bgmagic16") {
cfunc <- paste("sim_geno_", type, sep="")
if(type=="bgmagic16") n.gen <- 16
else n.gen <- as.numeric(substr(type, 3, 3))
one.map <- TRUE
if(xchr)
warning("sim.geno not working properly for the X chromosome for 4- or 8-way RIL.")
}
else if(type == "bcsft") {
one.map <- TRUE
cfunc <- "sim_geno_bcsft"
cross.scheme <- attr(cross, "scheme") ## c(s,t) for BC(s)F(t)
if(!xchr) {# autosomal
n.gen <- 3 - (cross.scheme[1] == 0)
}
else { # X chromsome
cross.scheme[1] <- cross.scheme[1] + cross.scheme[2] - (cross.scheme[1] == 0)
cross.scheme[2] <- 0
n.gen <- 2
}
}
else
stop("sim_geno not available for cross type ", type, ".")
# genotype data
gen <- cross$geno[[i]]$data
gen[is.na(gen)] <- 0
# recombination fractions
if(one.map) {
# recombination fractions
map <- create.map(cross$geno[[i]]$map,step,temp.offend,stepwidth)
rf <- mf(diff(map))
if(type=="risib" || type=="riself")
rf <- adjust.rf.ri(rf, sub("^ri", "", type), chr_type)
rf[rf < 1e-14] <- 1e-14
# new genotype matrix with pseudomarkers filled in
newgen <- matrix(ncol=length(map),nrow=nrow(gen))
dimnames(newgen) <- list(NULL,names(map))
newgen[,colnames(gen)] <- gen
newgen[is.na(newgen)] <- 0
n.pos <- ncol(newgen)
}
else {
map <- create.map(cross$geno[[i]]$map,step,temp.offend,stepwidth)
rf <- mf(diff(map[1,]))
rf[rf < 1e-14] <- 1e-14
rf2 <- mf(diff(map[1,]))
rf2[rf2 < 1e-14] <- 1e-14
# new genotype matrix with pseudomarkers filled in
newgen <- matrix(ncol=ncol(map),nrow=nrow(gen))
dimnames(newgen) <- list(NULL,colnames(map))
newgen[,colnames(gen)] <- gen
newgen[is.na(newgen)] <- 0
n.pos <- ncol(newgen)
}
# call C function
if(one.map) {
## Hide cross scheme in genoprob to pass to routine. BY
temp <- as.integer(rep(0,n.draws*n.ind*n.pos))
if(type == "bcsft")
temp[1:2] <- cross.scheme
z <- .C(cfunc,
as.integer(n.ind), # number of individuals
as.integer(n.pos), # number of markers
as.integer(n.draws), # number of simulation replicates
as.integer(newgen), # genotype data
as.double(rf), # recombination fractions
as.double(error.prob), #
draws=as.integer(temp),
PACKAGE="qtl")
cross$geno[[i]]$draws <- array(z$draws,dim=c(n.ind,n.pos,n.draws))
dimnames(cross$geno[[i]]$draws) <- list(NULL, names(map), NULL)
}
else {
z <- .C(cfunc,
as.integer(n.ind), # number of individuals
as.integer(n.pos), # number of markers
as.integer(n.draws), # number of simulation replicates
as.integer(newgen), # genotype data
as.double(rf), # recombination fractions
as.double(rf2), # recombination fractions
as.double(error.prob), #
draws=as.integer(rep(0,n.draws*n.ind*n.pos)),
PACKAGE="qtl")
cross$geno[[i]]$draws <- array(z$draws,dim=c(n.ind,n.pos,n.draws))
dimnames(cross$geno[[i]]$draws) <- list(NULL, colnames(map), NULL)
}
# attribute set to the error.prob value used, for later
# reference
attr(cross$geno[[i]]$draws, "map") <- map
attr(cross$geno[[i]]$draws,"error.prob") <- error.prob
attr(cross$geno[[i]]$draws,"step") <- step
attr(cross$geno[[i]]$draws,"off.end") <- temp.offend
attr(cross$geno[[i]]$draws,"map.function") <- map.function
attr(cross$geno[[i]]$draws,"stepwidth") <- stepwidth
}
# store simulated genotypes as integers
for(i in 1:nchr(cross))
storage.mode(cross$geno[[i]]$draws) <- "integer"
return(cross)
# 4- and 8-way RIL: reorganize the results
if(type=="ri4self" || type=="ri4sib" || type=="ri8self" || type=="ri8sib" || type=="bgmagic16")
cross <- reorgRIdraws(cross)
cross
}
# end of sim.geno.R
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.