| make.cdf.package {makecdfenv} | R Documentation |
This function reads an Affymetrix chip description file (CDF) and creates an R package that when loaded has the CDF environment available for use.
make.cdf.package(filename, packagename = NULL, cdf.path = getwd(), package.path = getwd(), compress = FALSE, author = "The Bioconductor Project", maintainer = "The Bioconductor Project <bioconductor@stat.math.ethz.ch>", version = library(help=makecdfenv)$info[[2]][[2]][2], unlink = FALSE, verbose = TRUE)
filename |
Character. Filename of the CDF file - without the path prefix! |
packagename |
Character. Name wanted for the package. |
cdf.path |
Character. Path to the CDF file. |
package.path |
Character. Path where the package will be created. |
compress |
Logical. If TRUE, CDF file is compressed. |
author |
Character. What to put in the author field of the package. |
maintainer |
Character. What to put in the maintainer field of the package. |
version |
Character. What to put in the version
field. Should be a of the form x.x.x. |
unlink |
Logical. If TRUE, and a package directory exists
already in package.path, that is overwritten. |
verbose |
Logical. If TRUE messages are shown. |
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
cleancdfname(abatch@cdfName) with abatch an
AffyBatch object obtained, for example, using
ReadAffy. This is the package name that the
affy package looks for by default.
If the user has a CEL file, called filename, the recommended
package name for the environment is
cleancdfname(whatcdf(filename)). This usually coincides with
the default.
Please see the vignette for more details.
If success, the function returns the name of the created package.
Rafael A. Irizarry, Wolfgang Huber
pkgpath <- tempdir()
make.cdf.package("Hu6800.CDF.gz",
cdf.path=system.file("extdata", package="makecdfenv"),
compress=TRUE,
package.path = pkgpath)
dir(pkgpath)