pdInfoBuilder: Platform Design Information Package Builder

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.

AuthorSeth Falcon, Vince Carey, Matt Settles, Kristof de Beuf, Benilton Carvalho
Date of publicationNone
MaintainerBenilton Carvalho <beniltoncarvalho@gmail.com>
LicenseArtistic-2.0
Version1.38.0

View on Bioconductor

Functions

AffyClariomSPDInfoPkgSeed-class Man page
AffyExonPDInfoPkgSeed-class Man page
AffyExpressionPDInfoPkgSeed-class Man page
AffyGenePDInfoPkgSeed-class Man page
AffySNPCNVPDInfoPkgSeed2-class Man page
AffySNPCNVPDInfoPkgSeed-class Man page
AffySNPPDInfoPkgSeed2-class Man page
AffySNPPDInfoPkgSeed-class Man page
AffyTilingPDInfoPkgSeed-class Man page
cdf2table Man page
chipName Man page
chipName,AffyExpressionPDInfoPkgSeed-method Man page
chipName,AffyGeneric1PDInfoPkgSeed-method Man page
chipName,AffySNPCNVPDInfoPkgSeed2-method Man page
chipName,AffySNPCNVPDInfoPkgSeed2-method Man page
chipName,AffySNPCNVPDInfoPkgSeed-method Man page
chipName,AffySNPCNVPDInfoPkgSeed-method Man page
chipName,AffySNPPDInfoPkgSeed2-method Man page
chipName,AffySNPPDInfoPkgSeed2-method Man page
chipName,AffySNPPDInfoPkgSeed-method Man page
chipName,AffySNPPDInfoPkgSeed-method Man page
chipName,AffySTPDInfoPkgSeed-method Man page
chipName,AffyTilingPDInfoPkgSeed-method Man page
chipName,NimbleGenPDInfoPkgSeed-method Man page
getGeometry Man page
getGeometry,AffyExpressionPDInfoPkgSeed-method Man page
getGeometry,AffySNPCNVPDInfoPkgSeed-method Man page
getGeometry,AffySNPCNVPDInfoPkgSeed-method Man page
getGeometry,AffySNPPDInfoPkgSeed-method Man page
getGeometry,AffySNPPDInfoPkgSeed-method Man page
getGeometry,AffySTPDInfoPkgSeed-method Man page
getGeometry,AffyTilingPDInfoPkgSeed-method Man page
getGeometry,NimbleGenPDInfoPkgSeed-method Man page
makePdInfoPackage Man page
makePdInfoPackage,AffyClariomSPDInfoPkgSeed-method Man page
makePdInfoPackage,AffyExonPDInfoPkgSeed-method Man page
makePdInfoPackage,AffyExpressionPDInfoPkgSeed-method Man page
makePdInfoPackage,AffyGenePDInfoPkgSeed-method Man page
makePdInfoPackage,AffyHTAPDInfoPkgSeed-method Man page
makePdInfoPackage,AffyMiRNAPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySNPCNVPDInfoPkgSeed2-method Man page
makePdInfoPackage,AffySNPCNVPDInfoPkgSeed2-method Man page
makePdInfoPackage,AffySNPCNVPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySNPCNVPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed2-method Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySTPDInfoPkgSeed-method Man page
makePdInfoPackage,AffyTilingPDInfoPkgSeed-method Man page
makePdInfoPackage,GenericPDInfoPkgSeed-method Man page
makePdInfoPackage,NgsExpressionPDInfoPkgSeed-method Man page
makePdInfoPackage,NgsTilingPDInfoPkgSeed-method Man page
NgsExpressionPDInfoPkgSeed-class Man page
NgsTilingPDInfoPkgSeed-class Man page
NimbleGenPDInfoPkgSeed-class Man page
sequenceParser Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.