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", ...)
.
cdfFile
:"files/Mapping250K_Nsp.cdf"
csvAnnoFile
:"files/Mapping250K_Nsp_annot.csv"
csvSeqFile
:Mapping250K_Nsp_probe_tab
.predictAccuracy
.crlmm
function.snprma
.chipName
:manufacturer
:genomebuild
:pdInfoObjectName
:geometry
:name
:version
:license
:author
:email
:url
:biocViews
:
Class "PDInfoPkgSeed"
, directly.
Class "PkgSeed"
, by class "PDInfoPkgSeed", distance 2.
See showMethods(classes="AffySNPPDInfoPkgSeed")
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.
Seth Falcon
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))