Description Objects from the Class Slots Methods Note Examples
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
: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
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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))
|
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