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\name{getAnnMap}
\alias{getAnnMap}
\title{Get annotation map}
\description{
This function retrieves a map object from an annotation data
package. It is intended to serve as a common interface for
obtaining map objects from both SQLite-based and environment-based
annotation data packages.
}
\usage{
getAnnMap(map, chip, load = TRUE, type = c("db", "env"))
}
\arguments{
\item{map}{a string specifying the name of the map to retrieve. For
example, \code{"ENTREZID"} or \code{"GO"}}
\item{chip}{a string describing the chip or genome}
\item{load}{a logical value. When \code{TRUE}, \code{getAnnMap}
will try to load the annotation data package if it is not
already attached.}
\item{type}{a character vector of one or more annotation data
package types. The currently supported types are \code{"db"} and
\code{"env"}. If \code{load} is \code{TRUE}, you can specify both
\code{"db"} and \code{"env"} and the order will determine which
type is tried first. This provides a fall-back mechanism when the
preferred annotation data package type is not available. If
\code{type} is missing, then the first matching annotation package
found in the search path will be used, and then the default value
of \code{type} takes over.}
}
\details{
\code{getAnnMap} uses the search path (see \code{search}) to find an
appropriate annotation data package; when called with
\code{chip="hgu95av2"}, the function will use the first hgu95av2
package on the search path whether it be db or environment-based. If
\code{load=TRUE} and no suitable package is found on the search path,
then the function will attempt to load an appropriate package. The
\code{type} argument is used to determine which type of package (db or
env) is loaded first.
}
\value{
If \code{type} is \code{"db"}, an S4 object representing the
requested map. If \code{type} is \code{"env"}, an R
\code{environment} object representing the requested map.
}
\author{Seth Falcon}
\examples{
map <- getAnnMap("ENTREZID", "hgu95av2", load=TRUE, type=c("env", "db"))
class(map)
}
\keyword{manip}
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