adding the new function 'where'

[ape.git] / man / where.Rd

diff --git a/man/where.Rd b/man/where.Rd
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+\names{where}
+\alias{where}
+\title{Find Patterns in DNA Sequences}
+\description{
+  This function finds patterns in a single or a set of DNA sequences.
+}
+\usage{
+where(x, pattern)
+}
+\arguments{
+  \item{x}{an object of class \code{"DNAbin"}.}
+  \item{pattern}{a character string to be searched in \code{x}.}
+}
+\details{
+  If \code{x} is a vector, the function returns a single vector giving
+  the position(s) where the pattern was found. If \code{x} is a matrix
+  or a list, it returns a list with the positions of the pattern for
+  each sequence.
+
+  Patterns may be overlapping. For instance, if \code{pattern = "tata"}
+  and the sequence starts with `tatata', then the vector returned will
+  be c(1, 3).
+}
+\value{
+  a vector of integers or a list of such vectors.
+}
+\author{Emmanuel Paradis}
+\seealso{
+  \code{\link{DNAbin}}, \code{\link{image.DNAbin}}
+}
+\examples{
+data(woodmouse)
+where(woodmouse, "tata")
+}
+\keyword{manip}