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clean.scantwo.Rd
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clean.scantwo.Rd
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\name{clean.scantwo}
\alias{clean.scantwo}
\title{Clean up scantwo output}
\description{
In an object output from \code{\link{scantwo}}, replaces negative
and missing LOD scores with 0, and replaces LOD scores for pairs of
positions that are not separated by \code{n.mar} markers, or that are
less than \code{distance} cM apart, with 0. Further, if the LOD
for full model is less than the LOD for the additive model, the
additive LOD is pasted over the full LOD.
}
\usage{
\method{clean}{scantwo}(object, n.mar=1, distance=0, \dots)
}
\arguments{
\item{object}{An object of class \code{scantwo}. See
\code{\link{scantwo}} for details.}
\item{n.mar}{Pairs of positions not separated by at least this many
markers have LOD scores set to 0.}
\item{distance}{Pairs of positions not separated by at least this
distance have LOD scores set to 0.}
\item{\dots}{Ignored at this point.}
}
\value{
The input scantwo object, with any negative or missing LOD scores
replaced by 0, and LOD scores for pairs of positions separated by
fewer than \code{n.mar} markers, or less than \code{distance} cM, are
set to 0.
Also, if the LOD for the full model is less than the LOD for the
additive model, the additive LOD is used in place of the full LOD.
}
\examples{
data(fake.f2)
\dontshow{fake.f2 <- subset(fake.f2, chr=18:19)}
fake.f2 <- calc.genoprob(fake.f2, step=5)
out2 <- scantwo(fake.f2, method="hk")
out2 <- clean(out2)
out2cl2 <- clean(out2, n.mar=2, distance=5)
}
\seealso{ \code{\link{scantwo}},
\code{\link{summary.scantwo}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{manip}