AffySNPPDInfoPkgSeed2-class: Class "AffySNPPDInfoPkgSeed2"

Description Objects from the Class Slots Methods Note Examples

Description

A generic annotation package builder for Affymetrix SNP 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("AffySNPPDInfoPkgSeed2", cdfFile, csvAnnoFile, csvSeqFile, ...).

Slots

axiom:

Logical flag for experimental build of annotation packages for Axiom arrays.

cdfFile:

CDF file for the design.

csvAnnoFile:

Affymetrix CSV Annotation file.

csvSeqFile:

Affymetrix 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 = "AffySNPPDInfoPkgSeed2"): ...

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.

Examples

1
showClass("AffySNPPDInfoPkgSeed2")

pdInfoBuilder documentation built on Nov. 8, 2020, 5:19 p.m.