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 = "Biocore Package Maintainer <maintainer@bioconductor.org>", version = packageDescription("makecdfenv", fields ="Version"), species = NULL, 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 |
author |
Character. What to put in the |
maintainer |
Character. What to put in the |
version |
Character. What to put in the version
field. Should be a of the form |
species |
Character. Must be specified using the format e.g., Homo\_sapiens |
unlink |
Logical. If |
verbose |
Logical. If |
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, species = "Homo_sapiens", package.path = pkgpath) dir(pkgpath)