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#####################################################################
#
# mqmcofactors.R
#
# Copyright (c) 2009-2010, Danny Arends
#
# Modified by Karl Broman and Pjotr Prins
#
#
# first written Februari 2009
# last modified April 2010
#
# 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: find.markerindex
# mqmsetcofactors
# mqmautocofactors
# scoremissingmarkers
# calculatedensity
# mqmplot.cofactors
# checkdistances
#
#####################################################################
######################################################################
#
# find.markerindex: Extracts the number of the marker when viewing the markers lineair
# mqmcofactors: Prepares a cofactor list to use with mqmscan
# mqmsetcofactors: Prepares a cofactor list to use with mqmscan
#
######################################################################
find.markerindex <- function(cross, name) {
match(name, markernames(cross))
}
mqmsetcofactors <- function(cross,each = NULL,cofactors=NULL,sexfactors=NULL,verbose=FALSE){
if(is.null(each) && is.null(cofactors))
stop("Please set either the each parameter or the cofactors")
if(missing(cross))
stop("No cross file. Please supply a valid cross object.")
individuals <- nind(cross)
n.chr <- nchr(cross)
n.mark <- sum(nmar(cross))
cofactorlist <- rep(0,n.mark)
if(!is.null(each) && each > n.mark)
stop("Not enough markers to place cofactors at this wide an interval.")
if(verbose) {
cat("INFO: Found",individuals,"individuals in the cross object.\n")
cat("INFO: Mamimum amount of cofactors",(individuals-15)," (each =",ceiling(sum(n.mark)/(individuals-15)),") leaves 15 Degrees of Freedom (no Dominance).\n")
cat("INFO: Mamimum amount of cofactors",(individuals-15)/2," (each =",ceiling(sum(n.mark)/(individuals-15))*2,") leaves 15 Degrees of Freedom (Dominance).\n")
}
if(is.null(cofactors)){
cofactorlist <- rep(c(rep(0,each-1),1),(2*n.mark)/each)
cofactorlist <- cofactorlist[1:n.mark]
}else{
if(max(cofactors) > n.mark)
stop("Trying to set a non-existent marker as a cofactor.")
if(min(cofactors) <= 0)
stop("Trying to set a non-existent marker as a cofactor.")
cofactorlist[cofactors]=1
if(!is.null(sexfactors)){
cofactorlist[sexfactors]=2
}
}
if(sum(cofactorlist) > (individuals-15)){
warning("Trying to set: ",ceiling(sum(n.mark)/each)," markers as cofactor. This leaves less than 15 Degrees of Freedom.\n")
}
cofactorlist
}
scoremissingmarkers <- function(cross){
genotype <- pull.geno(cross)
nind <- dim(genotype)[1]
missing <- NULL
for(x in 1:dim(genotype)[2]){
missing <- c(missing,sum(is.na(genotype[,x]))/nind)
}
missing
}
calculatedensity <- function(cross,distance=30){
genotype <- pull.geno(cross)
densities <- NULL
for(chr in 1:nchr(cross)){
map <- pull.map(cross)[[chr]]
for(x in 1:length(map)){
densities <- c(densities,sum(map[which(map > map[x]-distance)] < map[x]+distance))
}
}
densities
}
mqmautocofactors <- function(cross, num=50, distance=5,dominance=FALSE,plot=FALSE,verbose=FALSE){
if(num > (nind(cross)-15) && !dominance){
stop("Trying to set: ",num," markers as cofactor. This leaves less than 15 Degrees of Freedom.\n")
}
if(num > ((nind(cross)-15)/2) && dominance){
stop("Trying to set: ",num," markers as cofactor. This leaves less than 15 Degrees of Freedom.\n")
}
if(distance < 0.1){
distance <- 0.1
}
# r <- scanone(cross)
cofactors <- rep(0,sum(nmar(cross)))
missing <- scoremissingmarkers(cross)
densities <- calculatedensity(cross,distance*2)*missing
cnt <- 0
while(sum(cofactors) < num && cnt < num){
lefttoset <- num - sum(cofactors)
if(verbose) cat("Cofactors left",lefttoset,"/",num,"\n")
possible <- which(max(densities)==densities)
if(length(possible) > lefttoset){
possible <- sample(possible,lefttoset)
}
cofactors[possible] <- 1
densities[which(cofactors==1)] <- 0
cofactors <- checkdistances(cross,cofactors,distance)
cnt <- cnt+1
}
if(cnt==num && verbose) cat("Solution by iteration, there might be less cofactors then requested\n")
if(plot) mqmplot.cofactors(cross,cofactors)
cofactors
}
checkdistances <- function(cross,cofactors,dist=5){
map <- unlist(pull.map(cross))
newcofactors <- cofactors
cnt_dropped <- 0
for(x in which(cofactors==1)){
for(y in which(cofactors==1)){
if(x != y){
chr_x <- strsplit(names(map[x]),'.',fixed=TRUE)[[1]][1]
loc_x <- as.double(map[x])
chr_y <- strsplit(names(map[y]),'.',fixed=TRUE)[[1]][1]
loc_y <- as.double(map[y])
if(chr_x==chr_y && abs(loc_x-loc_y) < dist){
newcofactors[y] <- 0
cnt_dropped <- cnt_dropped+1
}
}
}
}
#cat("Dropped ",cnt_dropped," cofactors due to conflicting locations\n")
newcofactors
}
mqmplot.cofactors <- function(cross,cofactors,...){
map <- pull.map(cross)
qc <- NULL
qn <- NULL
qp <- NULL
mapnames <- NULL
for(x in 1:nchr(cross)){
mapnames <- c(mapnames,names(pull.map(cross)[[x]]))
}
chr <- 1
genotype <- pull.geno(cross)
for(x in 1:length(cofactors)){
if(x > sum(nmar(cross)[1:chr])){
chr <- chr+1
}
if(cofactors[x]>0){
qn <- c(qn, mapnames[x])
qc <- c(qc, as.character(names(map)[chr]))
qp <- c(qp, as.double(unlist(map)[x]))
}
}
plot(makeqtl(sim.geno(cross),qc,qp,qn),...)
}
# end of mqmcofactors.R
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