AffySNPCNVPDInfoPkgSeed2-class: Class "AffySNPCNVPDInfoPkgSeed2"
In benilton/pdInfoBuilder: Platform Design Information Package Builder

AffySNPCNVPDInfoPkgSeed2-class

R Documentation

Class "AffySNPCNVPDInfoPkgSeed2"

Description

A generic annotation package builder for Affymetrix SNP/CNV arrays. This is a simplified version of the annotation package and crlmm will *NOT* work for them.

Objects from the Class

Objects can be created by calls of the form new("AffySNPCNVPDInfoPkgSeed2", csvAnnoFileCnv, csvSeqFileCnv, ...).

Slots

cdfFile:: Path to the CDF file for this.
csvAnnoFile:: Path to the Affymetrix CSV annotation for the SNP probes.
csvSeqFile:: Path to the (SNP) probe sequence file.
csvAnnoFileCnv:: Path to the Affymetrix CSV annotation for the CNV probes.
csvSeqFileCnv:: Path to the (CNV) probe sequence file.
chipName:: Name of the chip or platform
manufacturer:: chip/platform manufacturer
url:: chip URL
genomebuild:: The genome build this platform is based upon.
organism:: organism for chip.
species:: species for chip.
version:: A character vector giving the version number of the package.
license:: The license of the package
author:: Author of the package
email:: An email address to use in the Maintainer field
biocViews:: Character data for the biocViews field of the DESCRIPTION file

Methods

chipName: signature(object = "AffySNPCNVPDInfoPkgSeed2"): ...
makePdInfoPackage: signature(object = "AffySNPCNVPDInfoPkgSeed2"): ...

Note

This is a simplified annotation package. CRLMM won't work for these objects.

The user may need to rename the columns or even add column names to the annotation and sequence files. In case problems are found, column names are suggested.