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\name{mqmplot.cofactors}
\alias{mqmplot.cofactors}
\title{Plot cofactors on the genetic map}
\description{
Plots cofactors as created by \code{\link{mqmsetcofactors}}
or \code{\link{mqmautocofactors}} on the genetic map.
}
\usage{
mqmplot.cofactors(cross,cofactors, \dots)
}
\arguments{
\item{cross}{
An object of class \code{cross}. See \code{\link{read.cross}} for details. % \crossobject
}
\item{cofactors}{
List of cofactors to be analysed in the QTL model. To set cofactors use \code{\link{mqmautocofactors}} or \code{mqmsetcofactors}}. % \mqmcofactors
\item{\dots}{Passed to \code{\link{plot.qtl}}}
}
\author{
Danny Arends \email{danny.arends@gmail.com} % \dannyauthor
}
\seealso{
\itemize{
% \input{"inst/doc/Sources/MQM/mqm/standard_seealso.txt"}
\item The MQM tutorial: \url{http://rqtl.org/tutorials/MQM-tour.pdf}
\item \code{\link{MQM}} - MQM description and references
\item \code{\link{mqmscan}} - Main MQM single trait analysis
\item \code{\link{mqmscanall}} - Parallellized traits analysis
\item \code{\link{mqmaugment}} - Augmentation routine for estimating missing data
\item \code{\link{mqmautocofactors}} - Set cofactors using marker density
\item \code{\link{mqmsetcofactors}} - Set cofactors at fixed locations
\item \code{\link{mqmpermutation}} - Estimate significance levels
\item \code{\link{scanone}} - Single QTL scanning
% -----^^ inst/doc/Sources/MQM/mqm/standard_seealso.txt ^^-----
}
}
\examples{
data(multitrait)
cof1 <- mqmsetcofactors(multitrait,20)
cof2 <- mqmsetcofactors(multitrait,10)
op <- par(mfrow=c(2,1))
mqmplot.cofactors(multitrait,cof1,col="blue")
mqmplot.cofactors(multitrait,cof2,col="blue")
op <- par(mfrow=c(1,1))
}
\keyword{ hplot }
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