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\name{calConservation-methods}
\docType{methods}
\alias{calConservation}
\alias{calConservation-methods}
\alias{calConservation,character,character-method}
\alias{calConservation,character,missing-method}
\alias{calConservation,DNAString,DNAString-method}
\alias{calConservation,DNAStringSet,missing-method}
\title{calConservation method}
\description{
Calculate the conservation score for a pairwise alignment given a smooth window size.
}
\usage{
calConservation(aln1, aln2, windowSize=51L, which="1")
}
\arguments{
\item{aln1}{
A \code{DNAString} object , a \code{DNAStringSet} or a \code{character} object,
which contains the pairwise alignments.
When the last two objects have a length of 2, the argument \code{aln2} can be missing.
}
\item{aln2}{
A \code{DNAString}, a \code{character} object or missing.
}
\item{windowSize}{
The size of the sliding window (in nucleotides) for calculating local conservation in the alignment. This should be an odd value.
}
\item{which}{
The conservation profile of Which sequence in the alignments is computed. It can be "1" or "2".
}
}
\value{
A \code{numeric} vector with the same length of alignment is returned.
}
\author{
Ge Tan
}
\seealso{
\code{\link{searchAln}}
}
\keyword{methods}
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