AffySNPPDInfoPkgSeed-class {pdInfoBuilder}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", ...).

Slots

cdfFile:
Path to the CDF file for this platform. Example: "files/Mapping250K_Nsp.cdf"
csvAnnoFile:
Path to the Affymetrix CSV annotation file. Example: "files/Mapping250K_Nsp_annot.csv"
csvSeqFile:
Path to the Affymetrix probe sequence file. Example: Mapping250K_Nsp_probe_tab
splineParamFile
Path to the spline parameters file used to compute the predicted accuracy of the the genotype calls. Used internally in .predictAccuracy.
crlmmInfoFile
Path to is data file containing regions data used by the crlmm function.
referenceDistFile
Path to a reference distribution file used in the normalization step. This is the reference used in snprma.
chipName:
Name of the chip or platform
manufacturer:
chip/platform manufacturer
genomebuild:
The genome build this platform is based upon.
pdInfoObjectName:
Name of the R object that will be made available in a generated pdInfo package.
geometry:
Used to describe the geometry of the platform.
name:
The name of the package.
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
url:
URL
biocViews:
Character data for the biocViews field of the DESCRIPTION file

Extends

Class "PDInfoPkgSeed", directly. Class "PkgSeed", by class "PDInfoPkgSeed", distance 2.

Methods

See showMethods(classes="AffySNPPDInfoPkgSeed")

Notes

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/data_store. When makePdInfoPackage is run, these files are simply copied to the inst/extdata directory of the generated package.

Author(s)

Seth Falcon

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))


[Package pdInfoBuilder version 1.2.0 Index]