AffySNPCNVPDInfoPkgSeed2-class: Class "AffySNPCNVPDInfoPkgSeed2"

In pdInfoBuilder: Platform Design Information Package Builder

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.

Author(s)

Benilton Carvalho

Examples

showClass("AffySNPCNVPDInfoPkgSeed2")

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