getProbeDataAffy {matchprobes}R Documentation

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 = TRUE)

Arguments

arraytype Character. Array type (e.g. 'HG-U133A')
datafile Character. The filename of the input data file. If omitted a default name is constructed from arraytype (see 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".)

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.

Value

A list with three components

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.

normal-bracket36bracket-normal

See Also

makeProbePackage

Examples

  ## Please refer to the vignette

[Package matchprobes version 1.2.1 Index]