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\name{droponemarker}
\alias{droponemarker}
\title{Drop one marker at a time and determine effect on genetic map}
\description{
Drop one marker at a time from a genetic map and calculate the change
in log likelihood and in the chromosome length, in order to identify
problematic markers.
}
\usage{
droponemarker(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)
}
\arguments{
\item{cross}{An object of class \code{cross}. See
\code{\link{read.cross}} for details.}
\item{chr}{A vector specifying which chromosomes to test for the
position of the marker. This should be a vector of character
strings referring to chromosomes by name; numeric values are
converted to strings. Refer to chromosomes with a preceding \code{-}
to have all chromosomes but those considered. A logical (TRUE/FALSE)
vector may also be used.}
\item{error.prob}{Assumed genotyping error rate used in the calculation
of the penetrance Pr(observed genotype | true genotype).}
\item{map.function}{Indicates whether to use the Haldane, Kosambi,
Carter-Falconer, or Morgan map function when converting genetic
distances into recombination fractions. (Ignored if m > 0.)}
\item{m}{Interference parameter for the chi-square model for
interference; a non-negative integer, with m=0 corresponding to no
interference. This may be used only for a backcross or intercross.}
\item{p}{Proportion of chiasmata from the NI mechanism, in the Stahl
model; p=0 gives a pure chi-square model. This may be used only for
a backcross or intercross.}
\item{maxit}{Maximum number of EM iterations to perform.}
\item{tol}{Tolerance for determining convergence.}
\item{sex.sp}{Indicates whether to estimate sex-specific maps; this is
used only for the 4-way cross.}
\item{verbose}{If TRUE, print information on progress; if > 1, print
even more information.}
}
\value{
A data frame (actually, an object of class \code{"scanone"}, so that
one may use \code{\link{plot.scanone}},
\code{\link{summary.scanone}}, etc.) with each row being a marker.
The first two columns are the chromosome ID and position. The third
column is a LOD score comparing the hypothesis that the marker is not
linked to the hypothesis that it belongs at that position.
In the case of a 4-way cross, with \code{sex.sp=TRUE}, there are two
additional columns with the change in the estimated female and male genetic lengths
of the respective chromosome, upon deleting that marker.
With \code{sex.sp=FALSE}, or for other types of crosses, there is one
additional column, with the change in estimated genetic length of the respective
chromosome, when the marker is omitted.
A well behaved marker will have a negative LOD score and a small
change in estimated genetic length. A poorly behaved marker will have a large
positive LOD score and a large change in estimated genetic length. But note
that dropping the first or last marker on a chromosome could result in
a large change in estimated length, even if they are not badly
behaved; for these markers one should focus on the LOD scores, with a large
positive LOD score being bad.
}
\author{Karl W Broman, \email{broman@wisc.edu} }
\examples{
data(fake.bc)
droponemarker(fake.bc, 7, error.prob=0, verbose=FALSE)
}
\seealso{ \code{tryallpositions}, \code{\link{est.map}}, \code{\link{ripple}},
\code{\link{est.rf}}, \code{\link{switch.order}},
\code{\link{movemarker}}, \code{\link{drop.markers}} }
\keyword{utilities}
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