make.cdf.package: 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 ", version      = packageDescription("makecdfenv", fields ="Version"), species      = NULL, unlink       = FALSE, verbose      = TRUE)

Arguments

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.

Value

If success, the function returns the name of the created package.

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 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.

Examples

Run this code

  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)