get3primeIVTprobefileData: Read a data file describing the probe sequences on an...

In GCSscore: GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Description

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

Usage

get3primeIVTprobefileData(arraytype, datafile, pkgname, chip.pd, comparewithcdf = FALSE)

Arguments

arraytype	Character. Array type (e.g. 'HG-U133A')
datafile	Character. 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.
chip.pd	Character. Name of the platform design file for the 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 makeProbePackageGCSs 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 'probesetid', 'fsetid', 'fid', 'x', 'y', and 'GC.count'. 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.

See Also

makeProbePackageGCSs

Examples

if (length(list.files(path = ".", pattern = "*.CEL")) != 0){
  ## Example using the "Mouse430 2.0" chip-type
  
  ## Input the clean name for the given chip:
  chip <- "mouse4302"

  ## Input the .probe_tab file, as generated using the internal function:
     ##  IVT3primepFBuilder()
  
  probedata <- "GCSs.mouse4302.probeFile.probe_tab"
  
  ## Run function:
  get3primeIVTprobefileData(arraytype = chip, datafile = probedata)
  }

GCSscore documentation built on Nov. 8, 2020, 7:47 p.m.