make.cdf.env: CDF Environment Maker

Description

Reads an Affymetrix chip description file (CDF) and creates an environment used as a hash table for the probe set mapping to location.

Usage

make.cdf.env(filename, cdf.path = getwd(), compress = FALSE, return.env.only = TRUE, verbose = TRUE)

Arguments

filename

Character. Filename of the CDF file - without the path prefix!

cdf.path

Character. Path to the CDF file.

compress

Logical. If TRUE, CDF file is compressed.

return.env.only

Logical. If TRUE (the default), then the function returns an environment. Otherwise, a list with two elements, the first being the environment, and the second being a data structure that contains additional information needed for the package builder (see details, and vignette).

verbose

Logical. If TRUE, messages are shown.

Value

return.env.only, either the environment, or a list with two elements, env and syms. See details.

Details

Normally, this function should not be called directly. The preferred way to handle CDF information is to use make.cdf.package to build a package, and to install it into R. The CDF information can then either be invoked automatically by the package affy, or can be loaded manually by calling, for example, library(hgu133a). Some R installations (typically on Windows) do not offer all the tools that are necessary for package building. In such situations, this function may be called directly. Please see the vignette for details - type:

openVignette("makecdfenv")

Return values: env is an environment, used as a hash table. For every probe set name we have a matrix with 2 columns. The first column contains the PM locations and the second column the MM locations. For PM only chips the MM column will have NAs. syms is a list that contains chip-specific (i.e., CDF-file specific) information that can be used in the construction of the help files for the CDF package.

Examples

Run this code

  env <- make.cdf.env("Hu6800.CDF.gz",
           cdf.path=system.file("extdata", package="makecdfenv"),
           compress=TRUE)
  length(ls(env))
  get("U53347_at", env)