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\name{replaceqtl}
\alias{replaceqtl}
\title{Replace a QTL in a qtl object with a different position.}
\description{
This function replaces a QTL or QTLs in a qtl object with a different
position.
}
\usage{
replaceqtl(cross, qtl, indextodrop, chr, pos, qtl.name, drop.lod.profile=TRUE)
}
\arguments{
\item{cross}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details.}
\item{qtl}{A qtl object, as created by \code{\link[qtl]{makeqtl}}.}
\item{indextodrop}{Numeric index indicating the QTL to be replaced.}
\item{chr}{Vector (of same length as \code{indextodrop}) indicating the
chromosomes for the new QTL.}
\item{pos}{Vector (of same length as \code{indextodrop}) indicating the
positions for the new QTL. If there is no marker or pseudomarker at a
position, the nearest position is used.}
\item{qtl.name}{Optional vector (of same length as \code{indextodrop})
of user-specified names for each new QTL, used in the
drop-one-term ANOVA table in \code{\link[qtl]{fitqtl}}.
If unspecified, the names will be of the form \code{"Chr1@10"} for a
QTL on Chromsome 1 at 10 cM.}
\item{drop.lod.profile}{If TRUE, remove any LOD profiles from the object.}
}
\value{
The input \code{qtl} object,
but with some QTL replaced by new ones. See \code{\link[qtl]{makeqtl}} for
details on the format.
}
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu}}
\examples{
data(fake.f2)
# take out several QTLs and make QTL object
qc <- c(1, 6, 13)
qp <- c(25.8, 33.6, 18.63)
fake.f2 <- subset(fake.f2, chr=qc)
\dontshow{fake.f2 <- subset(fake.f2, ind=1:50)}
fake.f2 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp, what="draws")
qtl <- replaceqtl(fake.f2, qtl, 2, 6, 48.1)
}
\seealso{ \code{\link[qtl]{makeqtl}}, \code{\link[qtl]{fitqtl}},
\code{\link[qtl]{dropfromqtl}}, \code{\link[qtl]{addtoqtl}},
\code{\link[qtl]{reorderqtl}} }
\keyword{utilities}
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