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\name{make.cdf.package}
\alias{make.cdf.package}
\title{CDF Environment Package Maker}
\description{
This function reads an Affymetrix chip description file (CDF) and
creates an R package that when loaded has the CDF environment available
for use.}
\usage{
make.cdf.package(filename,
packagename = NULL,
cdf.path = getwd(),
package.path = getwd(),
compress = FALSE,
author = "The Bioconductor Project",
maintainer = "Biocore Package Maintainer <maintainer@bioconductor.org>",
version = packageDescription("makecdfenv", fields ="Version"),
species = NULL,
unlink = FALSE,
verbose = TRUE)
}
\arguments{
\item{filename}{Character. Filename of the CDF file -
\bold{without} the path prefix!}
\item{packagename}{Character. Name wanted for the package.}
\item{cdf.path}{Character. Path to the CDF file.}
\item{package.path}{Character. Path where the package will be created.}
\item{compress}{Logical. If \code{TRUE}, CDF file is compressed.}
\item{author}{Character. What to put in the \code{author} field of the package.}
\item{maintainer}{Character. What to put in the \code{maintainer} field of the package.}
\item{version}{Character. What to put in the version
field. Should be a of the form \code{x.x.x}.}
\item{species}{Character. Must be specified using the format e.g., Homo\_sapiens}
\item{unlink}{Logical. If \code{TRUE}, and a package directory exists
already in \code{package.path}, that is overwritten.}
\item{verbose}{Logical. If \code{TRUE} messages are shown.}
}
\details{The function is called for its side effect, creating a package.
By default the package name will be the name of the CDF file made lower
case and with special characters removed (i.e. only
alpha-numeric).
In general one would want to use the name given in by
\code{cleancdfname(abatch@cdfName)} with \code{abatch} an
\code{\link[affy:AffyBatch-class]{AffyBatch}} object obtained, for
example, using \code{\link[affy:read.affybatch]{ReadAffy}}. This is the
package name that the
\code{affy} package looks for by default.
If the user has a CEL file, called \code{filename}, the recommended
package name for the environment is
\code{cleancdfname(whatcdf(filename))}. This usually coincides with
the default.
Please see the vignette for more details.
}
\value{
If success, the function returns the name of the created package.
}
\seealso{\code{\link{make.cdf.env}}}
\author{Rafael A. Irizarry, Wolfgang Huber}
\examples{
pkgpath <- tempdir()
make.cdf.package("Hu6800.CDF.gz",
cdf.path=system.file("extdata", package="makecdfenv"),
compress=TRUE, species = "Homo_sapiens",
package.path = pkgpath)
dir(pkgpath)
}
\keyword{manip}
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