| AffySNPPDInfoPkgSeed-class {pdInfoBuilder} | R Documentation |
This class represents Platform Design (PD) packages for Affymetrix mapping (SNP chip) arrays.
Objects can be created by calls of the form new("AffySNPPDInfoPkgSeed", splineParamFile, crlmmInfoFile, referenceDistFile, ...).
splineParamFile:crlmmInfoFile:crlmm function.referenceDistFile:snprma.cdfFile:csvAnnoFile:csvSeqFile:chipName:manufacturer:url:genomebuild:organism:species:version:license:author:email:biocViews:signature(object = "AffySNPPDInfoPkgSeed"): ... signature(object = "AffySNPPDInfoPkgSeed"): ... signature(object = "AffySNPPDInfoPkgSeed"): ... *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.
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))