make.cdf.package {makecdfenv}R Documentation

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   = "The Bioconductor Project <bioconductor@stat.math.ethz.ch>",
  version      = packageDescription("makecdfenv", field="Version"),
  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.
unlink Logical. If TRUE, and a package directory exists already in package.path, that is overwritten.
verbose Logical. If 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 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.

Value

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

Author(s)

Rafael A. Irizarry, Wolfgang Huber

See Also

make.cdf.env

Examples

  pkgpath <- tempdir()
  make.cdf.package("Hu6800.CDF.gz",
           cdf.path=system.file("extdata", package="makecdfenv"),
           compress=TRUE,
           package.path = pkgpath)
  dir(pkgpath)     

[Package makecdfenv version 1.8.0 Index]