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######################################################################
#
# droponemarker.R
#
# copyright (c) 2019, Karl W Broman
# last modified Dec, 2019
# first written Oct, 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: droponemarker
#
######################################################################
######################################################################
#
# droponemarker: Drop one marker at a time from a genetic map, to
# evaluate the change in log likelihood and in map
# length, in order to identify problematic markers
#
######################################################################
droponemarker <-
function(cross, chr, error.prob=0.0001,
map.function=c("haldane", "kosambi", "c-f", "morgan"),
m=0, p=0, maxit=4000, tol=1e-6, sex.sp=TRUE, verbose=TRUE)
{
if(!inherits(cross, "cross"))
stop("Input must have class \"cross\".")
if(!missing(chr)) cross <- subset(cross, chr=chr)
if(any(nmar(cross) < 3)) {
if(all(nmar(cross) < 3))
stop("No chromosomes with at least three markers\n")
todrop <- names(cross$geno)[nmar(cross) < 3]
tokeep <- names(cross$geno)[nmar(cross) > 2]
warning("Dropping chr with <3 markers: ", paste(todrop, collapse=", "))
cross <- subset(cross, chr=tokeep)
}
map.function <- match.arg(map.function)
if(verbose) cat(" -Re-estimating map\n")
origmap <- est.map(cross, error.prob=error.prob, map.function=map.function,
m=m, p=p, maxit=maxit, tol=tol, sex.sp=sex.sp)
cross <- replace.map(cross, origmap)
origmaptab <- pull.map(cross, as.table=TRUE)
origmaptab <- cbind(origmaptab, LOD=rep(NA, nrow(origmaptab)))
if(is.matrix(origmap[[1]])) {
origmaptab <- cbind(origmaptab, Ldiff.female=rep(NA, nrow(origmaptab)),
Ldiff.male=rep(NA, nrow(origmaptab)))
sexsp <- TRUE
}
else {
origmaptab <- cbind(origmaptab, Ldiff=rep(NA, nrow(origmaptab)))
sexsp <- FALSE
}
for(i in names(cross$geno)) {
if(sexsp) {
Lf <- diff(range(origmap[[i]][1,]))
Lm <- diff(range(origmap[[i]][2,]))
}
else L <- diff(range(origmap[[i]]))
if(verbose) cat(" -Chromosome", i, "\n")
mnames <- markernames(cross, chr=i)
temp <- subset(cross, chr=i)
for(j in seq(along=mnames)){
if(verbose > 1) cat(" ---Marker", j, "of", length(mnames), "\n")
markerll <- markerloglik(cross, mnames[j], error.prob)
newmap <- est.map(drop.markers(temp, mnames[j]), error.prob=error.prob,
map.function=map.function, m=m, p=p, maxit=maxit, tol=tol,
sex.sp=sex.sp)
if(sexsp) {
origmaptab[mnames[j],4] <- -(attr(origmap[[i]], "loglik") - markerll - attr(newmap[[1]], "loglik"))/log(10)
origmaptab[mnames[j],5] <- Lf - diff(range(newmap[[1]][1,]))
origmaptab[mnames[j],6] <- Lm - diff(range(newmap[[1]][2,]))
}
else {
origmaptab[mnames[j],3] <- -(attr(origmap[[i]], "loglik") - markerll - attr(newmap[[1]], "loglik"))/log(10)
origmaptab[mnames[j],4] <- L - diff(range(newmap[[1]]))
}
}
}
class(origmaptab) <- c("scanone", "data.frame")
origmaptab$chr <- factor(origmaptab$chr, levels=unique(origmaptab$chr))
origmaptab
}
# end of droponemarker.R
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