make.cdf.package: CDF Environment Package Maker
In makecdfenv: CDF Environment Maker

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/make.cdf.env.R

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 `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`.
`species`	Character. Must be specified using the format e.g., Homo\_sapiens
`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

make.cdf.env

  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)