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\name{plotLodProfile}
\alias{plotLodProfile}
\title{Plot 1-d LOD profiles for a multiple QTL model}
\description{
Use the results of \code{\link[qtl]{refineqtl}} to plot
one-dimensional LOD profiles for each QTL.
}
\usage{
plotLodProfile(qtl, chr, incl.markers=TRUE, gap=25, lwd=2, lty=1, col="black",
qtl.labels=TRUE, mtick=c("line", "triangle"),
show.marker.names=FALSE, alternate.chrid=FALSE,
add=FALSE, \dots)
}
\arguments{
\item{qtl}{An object of class \code{"qtl"}; must have been produced by
\code{\link[qtl]{refineqtl}} using \code{keeplodprofiles=TRUE}.}
\item{chr}{Optional vector specifying which chromosomes to plot. (The
chromosomes must be specified by name.)}
\item{incl.markers}{Indicate whether to plot line segments at the
marker locations.}
\item{gap}{Gap separating chromosomes (in cM).}
\item{lwd}{Line widths for each QTL trace (length 1 or the number of QTL).}
\item{lty}{Line types for each QTL trace (length 1 or the number of QTL).}
\item{col}{Line col for each QTL trace (length 1 or the number of QTL).}
\item{qtl.labels}{If TRUE, place a label on each QTL trace.}
\item{mtick}{Tick mark type for markers (line segments or
upward-pointing triangels).}
\item{show.marker.names}{If TRUE, show the marker names along the x axis.}
\item{alternate.chrid}{If TRUE and more than one chromosome is
plotted, alternate the placement of chromosome
axis labels, so that they may be more easily distinguished.}
\item{add}{If TRUE, add curves to a current plot.}
\item{\dots}{Passed to the function \code{\link[graphics]{plot}} when it
is called.}
}
\value{None.}
\details{
The function plots LOD profiles in the context of a multiple QTL
model, using a scheme best described in Zeng et al. (2000). The
position of each QTL is varied, keeping all other loci fixed. If a
QTL is isolated on a chromosome, the entire chromosome is scanned; if
there are additional linked QTL, the position of a QTL is scanned over
the largest interval possible without allowing the order of QTLs along
a chromosome to change. At each position for the QTL being scanned,
we calculate a LOD score comparing the full model, with the QTL of
interest at that particular position (and all others at their fixed
positions) to the model with the QTL of interest (and any
interactions that include that QTL) omitted.
Care should be take regarding the arguments \code{lwd}, \code{lty},
and \code{col}; if vectors are given, they should be in the order of
the QTL within the object, which may be different than the order in
which they are plotted. (The LOD profiles are sorted by chromosome
and position.)
}
\examples{
data(fake.bc)
\dontshow{fake.bc <- subset(fake.bc, chr=c(2,5))}
fake.bc <- calc.genoprob(fake.bc, step=2)
qtl <- makeqtl(fake.bc, chr=c(2,5), pos=c(32.5, 17.5), what="prob")
out <- scanone(fake.bc, method="hk")
# refine QTL positions and keep LOD profiles
rqtl <- refineqtl(fake.bc, qtl=qtl, method="hk", keeplodprofile=TRUE)
# plot the LOD profiles
plotLodProfile(rqtl)
# add the initial scan results, for comparison
plot(out, add=TRUE, chr=c(2,5), col="red")
}
\seealso{ \code{\link[qtl]{refineqtl}},
\code{\link[qtl]{makeqtl}}, \code{\link[qtl]{scanqtl}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\references{
Zeng Z.-B., Liu, J., Stam, L. F., Kao, C.-H., Mercer, J. M. and
Laurie, C. C. (2000) Genetic architecture of a morphological shape
difference between two Drosophila species. \emph{Genetics} \bold{154},
299--310.
}
\keyword{hplot}
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