getProbeDataAffy: Read a data file describing the probe sequences on an Affymetrix genechip

Description

Read a data file describing the probe sequences on an Affymetrix genechip

Usage

getProbeDataAffy(arraytype, datafile, pkgname = NULL, comparewithcdf = FALSE)

Arguments

arraytype

Character. Array type (e.g. 'HG-U133A')

datafile

Character with the filename of the input data file, or a connection (see example). If omitted a default name is constructed from arraytype (for details you will need to consult this function's source code).

pkgname

Character. Package name. If NULL the name is derived from arraytype.

comparewithcdf

Logical. If TRUE, run a consistency check against a CDF package of the same name (what used to be Laurent's "extraparanoia".)

Value

dataEnv: an environment which contains the data frame with the probe sequences and the other probe data.
symVal: a named list of symbol value substitutions which can be used to customize the man pages. See createPackage.
pkgname: a character with the package name; will be the same as the function parameter pkgname if it was specified; otherwise, the name is constructed from the parameter arraytype.

Details

This function serves as an interface between the (1) representation of array probe information data in the packages that are generated by makeProbePackage and (2) the vendor- and possibly version-specific way the data are represented in datafile.

datafile is a tabulator-separated file with one row per probe, and column names 'Probe X', 'Probe Y', 'Probe Sequence', and 'Probe.Set.Name'. See the vignette for an example.

Examples

Run this code

  ## Please refer to the vignette