pdInfoBuilder: Platform Design Information Package Builder

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Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.

Author
Seth Falcon, Vince Carey, Matt Settles, Kristof de Beuf, Benilton Carvalho
Date of publication
None
Maintainer
Benilton Carvalho <beniltoncarvalho@gmail.com>
License
Artistic-2.0
Version
1.38.0

View on Bioconductor

Man pages

AffyClariomSPDInfoPkgSeed-class
Class "AffyClariomSPDInfoPkgSeed"
AffyExpressionPDInfoPkgSeed-class
Class "AffyExpressionPDInfoPkgSeed"
AffySNPCNVPDInfoPkgSeed2-class
Class "AffySNPCNVPDInfoPkgSeed2"
AffySNPCNVPDInfoPkgSeed-class
Class "AffySNPCNVPDInfoPkgSeed"
AffySNPPDInfoPkgSeed2-class
Class "AffySNPPDInfoPkgSeed2"
AffySNPPDInfoPkgSeed-class
Class "AffySNPPDInfoPkgSeed"
AffySTPDInfoPkgSeed-class
Class "AffySTPDInfoPkgSeed" for the Sense Target gene-level...
AffyTilingPDInfoPkgSeed-class
Class "AffyTilingPDInfoPkgSeed"
chipName
Return an Official Chip/Platform Name
GenericArrayFunctions
Helper functions to assist the creation of an annotation...
getGeometry
Return the Chip/Platform geometry
makePdInfoPackage
Create a Platform Design Info Package
NgsExpressionPDInfoPkgSeed-class
Class "NgsExpressionPDInfoPkgSeed"
NgsTilingPDInfoPkgSeed-class
Class "NgsTilingPDInfoPkgSeed"
NimbleGenPDInfoPkgSeed-class
Class "NimbleGenPDInfoPkgSeed"

Files in this package

pdInfoBuilder/.Rinstignore
pdInfoBuilder/CHANGES
pdInfoBuilder/DESCRIPTION
pdInfoBuilder/NAMESPACE
pdInfoBuilder/R
pdInfoBuilder/R/AllClasses.R
pdInfoBuilder/R/AllGenerics.R
pdInfoBuilder/R/chipName-methods.R
pdInfoBuilder/R/getGeometry-methods.R
pdInfoBuilder/R/initDb.R
pdInfoBuilder/R/initDb.snp6.R
pdInfoBuilder/R/initialize-methods.R
pdInfoBuilder/R/loaders.R
pdInfoBuilder/R/loaders.snp6.R
pdInfoBuilder/R/makePdInfoPackage-methods.R
pdInfoBuilder/R/pdBuilderV2AffyExpressionHT.R
pdInfoBuilder/R/pdBuilderV2AffySNP.R
pdInfoBuilder/R/pdBuilderV2AffySNPCNV.R
pdInfoBuilder/R/pdBuilderV2AffyTiling.R
pdInfoBuilder/R/pdBuilderV2Clariom.R
pdInfoBuilder/R/pdBuilderV2ExonTranscription.R
pdInfoBuilder/R/pdBuilderV2Gene.R
pdInfoBuilder/R/pdBuilderV2HTA2.R
pdInfoBuilder/R/pdBuilderV2NgsExpression.R
pdInfoBuilder/R/pdBuilderV2TiledRegion.R
pdInfoBuilder/R/pdBuilderV2miRNA.R
pdInfoBuilder/R/pdBuilderV3GenericArray.R
pdInfoBuilder/R/pmmmBlockToMat.R
pdInfoBuilder/R/schema.R
pdInfoBuilder/R/utils.R
pdInfoBuilder/TODO
pdInfoBuilder/build
pdInfoBuilder/build/vignette.rds
pdInfoBuilder/inst
pdInfoBuilder/inst/NEWS.Rd
pdInfoBuilder/inst/doc
pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.Rnw
pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf
pdInfoBuilder/inst/doc/Makefile
pdInfoBuilder/inst/doc/howto-AffymetrixMapping.R
pdInfoBuilder/inst/doc/howto-AffymetrixMapping.Rnw
pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf
pdInfoBuilder/inst/pd.PKG.template
pdInfoBuilder/inst/pd.PKG.template/DESCRIPTION
pdInfoBuilder/inst/pd.PKG.template/NAMESPACE
pdInfoBuilder/inst/pd.PKG.template/R
pdInfoBuilder/inst/pd.PKG.template/R/all.R
pdInfoBuilder/inst/pd.PKG.template/inst
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/Makefile
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/checkTables_test.R
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/crlmm_test.R
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/runall.sh
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/runalltests.R
pdInfoBuilder/inst/pd.PKG.template/inst/UnitTests/runfile.sh
pdInfoBuilder/inst/pd.PKG.template/man
pdInfoBuilder/inst/pd.PKG.template/man/pkg.Rd
pdInfoBuilder/inst/pd.PKG.template/man/probeSequences.Rd
pdInfoBuilder/inst/pd.PKG.template2
pdInfoBuilder/inst/pd.PKG.template2/DESCRIPTION
pdInfoBuilder/inst/pd.PKG.template2/NAMESPACE
pdInfoBuilder/inst/pd.PKG.template2/R
pdInfoBuilder/inst/pd.PKG.template2/R/all.R
pdInfoBuilder/inst/pd.PKG.template2/inst
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/Makefile
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/checkTables_test.R
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/crlmm_test.R
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/runall.sh
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/runalltests.R
pdInfoBuilder/inst/pd.PKG.template2/inst/UnitTests/runfile.sh
pdInfoBuilder/inst/pd.PKG.template2/man
pdInfoBuilder/inst/pd.PKG.template2/man/pkg.Rd
pdInfoBuilder/inst/pdBuilders
pdInfoBuilder/inst/pdBuilders/AMakefile
pdInfoBuilder/inst/pdBuilders/README
pdInfoBuilder/inst/pdBuilders/runPDIB250kNsp.R
pdInfoBuilder/inst/pdBuilders/runPDIB250kSty.R
pdInfoBuilder/inst/pdBuilders/runPDIB50kHind.R
pdInfoBuilder/inst/pdBuilders/runPDIB50kXba.R
pdInfoBuilder/inst/pdBuilders/runPDIBSnp5.R
pdInfoBuilder/inst/pdBuilders/runPDIBSnp6.R
pdInfoBuilder/inst/scripts
pdInfoBuilder/inst/scripts/BuildingPDInfoPkgs.Rnw
pdInfoBuilder/inst/scripts/BuildingPDInfoPkgs.pdf
pdInfoBuilder/man
pdInfoBuilder/man/AffyClariomSPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/AffyExpressionPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/AffySNPCNVPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/AffySNPCNVPDInfoPkgSeed2-class.Rd
pdInfoBuilder/man/AffySNPPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/AffySNPPDInfoPkgSeed2-class.Rd
pdInfoBuilder/man/AffySTPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/AffyTilingPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/GenericArrayFunctions.Rd
pdInfoBuilder/man/NgsExpressionPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/NgsTilingPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/NimbleGenPDInfoPkgSeed-class.Rd
pdInfoBuilder/man/chipName.Rd
pdInfoBuilder/man/getGeometry.Rd
pdInfoBuilder/man/makePdInfoPackage.Rd
pdInfoBuilder/src
pdInfoBuilder/src/pdInfoBuilder.c
pdInfoBuilder/src/pdInfoBuilder.h
pdInfoBuilder/vignettes
pdInfoBuilder/vignettes/BuildingPDInfoPkgs.Rnw
pdInfoBuilder/vignettes/Makefile
pdInfoBuilder/vignettes/howto-AffymetrixMapping.Rnw