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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pdInfoBuilder")
AuthorSeth Falcon, Vince Carey, Matt Settles, Kristof de Beuf, Benilton Carvalho
Bioconductor views Annotation Infrastructure
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,AffySNPCNVPDInfoPkgSeed-method Man page
chipName,AffySNPPDInfoPkgSeed2-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,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,AffySNPCNVPDInfoPkgSeed-method Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed2-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

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

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

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

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