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))