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

AffySNPPDInfoPkgSeed-class

R Documentation

Class "AffySNPPDInfoPkgSeed"

Description

This class represents Platform Design (PD) packages for Affymetrix mapping (SNP chip) arrays.

Objects from the Class

Objects can be created by calls of the form new("AffySNPPDInfoPkgSeed", splineParamFile, crlmmInfoFile, referenceDistFile, ...).

Slots

splineParamFile:: Spline parameters file used to compute the predicted accuracy of the genotype calls.
crlmmInfoFile:: Data file containing regions data used by the crlmm function.
referenceDistFile:: Reference distribution file used in the normalization step by snprma.
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 = "AffySNPPDInfoPkgSeed"): ...
getGeometry: signature(object = "AffySNPPDInfoPkgSeed"): ...
makePdInfoPackage: signature(object = "AffySNPPDInfoPkgSeed"): ...

Note

*IMPORTANT* The user is strongly advised to download Affymetrix SNP packages from BioConductor.

The files used for slots splineParamFile, crlmmInfoFile, and referenceDistFile are generated by the Bioconductor project for each chip/platform and are hosted in our svn data repository at https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store. When makePdInfoPackage is run, these files are simply copied to the inst/extdata directory of the generated package.

Examples

showClass("AffySNPPDInfoPkgSeed")

cdfFile <- "Mapping250K_Nsp.cdf"
csvAnno <- "Mapping250K_Nsp_annot.csv"
csvSeq <- "Mapping250K_Nsp_probe_tab"

spline <- "pd.mapping250k.nsp.spline.params.rda"
refd <- "pd.mapping250k.nspRef.rda"
crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda"

pkg <- new("AffySNPPDInfoPkgSeed", 
           version="0.1.5",
           author="A. U. Thor", email="au@thor.net",
           biocViews="AnnotationData",
           genomebuild="NCBI Build 35, May 2004",
           cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq,
           splineParamFile=spline, crlmmInfoFile=crlmmInf,
           referenceDistFile=refd)

showMethods(classes=class(pkg))

benilton/pdInfoBuilder documentation built on July 3, 2024, 12:23 p.m.