pdInfoBuilder: Platform Design Information Package Builder
Version 1.40.0

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.

Browse man pages Browse package API and functions Browse package files

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
Version1.40.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pdInfoBuilder")

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"

Functions

AffyClariomSPDInfoPkgSeed-class Man page
AffyExonPDInfoPkgSeed-class Man page
AffyExpressionPDInfoPkgSeed-class Man page
AffyGenePDInfoPkgSeed-class Man page
AffySNPCNVPDInfoPkgSeed-class Man page
AffySNPCNVPDInfoPkgSeed2-class Man page
AffySNPPDInfoPkgSeed-class Man page
AffySNPPDInfoPkgSeed2-class Man page
AffyTilingPDInfoPkgSeed-class Man page
NgsExpressionPDInfoPkgSeed-class Man page
NgsTilingPDInfoPkgSeed-class Man page
NimbleGenPDInfoPkgSeed-class Man page
annot2fdata Source code
atomIdxToProbeIdx Source code
buildPdInfoDb Source code
cdf2table Man page Source code
cdfUnits2table Source code
checkFields Source code
chipName Man page
chipName,AffyExpressionPDInfoPkgSeed-method Man page
chipName,AffyGeneric1PDInfoPkgSeed-method Man page
chipName,AffySNPCNVPDInfoPkgSeed-method Man page Man page
chipName,AffySNPCNVPDInfoPkgSeed2-method Man page Man page
chipName,AffySNPPDInfoPkgSeed-method Man page Man page
chipName,AffySNPPDInfoPkgSeed2-method Man page Man page
chipName,AffySTPDInfoPkgSeed-method Man page
chipName,AffyTilingPDInfoPkgSeed-method Man page
chipName,NimbleGenPDInfoPkgSeed-method Man page
closeDb Source code
combineIdx Source code
combinePgfClfProbesetsMps Source code
combinePgfClfProbesetsMps0 Source code
combinePgfClfProbesetsMpsHTA Source code
connectDb Source code
createChrDict Source code
createFeatureTableInfo Source code
createIndicesDb Source code
createSeqMat Source code
createSeqMat.cnv Source code
createTableInfoTable Source code
dbCreateIndex Source code
dbCreateIndicesBg Source code
dbCreateIndicesBgTiling Source code
dbCreateIndicesCnvPm Source code
dbCreateIndicesFs Source code
dbCreateIndicesFsCnv Source code
dbCreateIndicesMm Source code
dbCreateIndicesPm Source code
dbCreateIndicesPmTiling Source code
dbCreateIndicesSnpPm Source code
dbCreateTable Source code
dbCreateTableInfo Source code
dbInsertDataFrame Source code
dxToIdx Source code
fixManFsetid Source code
getAllFSetMpsTables Source code
getFSetMpsTables Source code
getFragLength.na29 Source code
getFragmentLengthTable Source code
getGeometry Man page
getGeometry,AffyExpressionPDInfoPkgSeed-method Man page
getGeometry,AffySNPCNVPDInfoPkgSeed-method Man page Man page
getGeometry,AffySNPPDInfoPkgSeed-method Man page Man page
getGeometry,AffySTPDInfoPkgSeed-method Man page
getGeometry,AffyTilingPDInfoPkgSeed-method Man page
getGeometry,NimbleGenPDInfoPkgSeed-method Man page
getKeys Source code
getLevelSchema Source code
getSchema Source code
getSchemaAndKeys Source code
getTotalFSetTables Source code
getTypeSchema Source code
getUniqueProbesTables Source code
groupDirectionToInt Source code
increaseDbPerformance Source code
initDb Source code
insertInFragmentLengthTable Source code
loadAffyCsv Source code
loadAffySeqCsv Source code
loadUnitNames Source code
loadUnits Source code
loadUnitsByBatch Source code
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,AffySNPCNVPDInfoPkgSeed-method Man page Man page
makePdInfoPackage,AffySNPCNVPDInfoPkgSeed2-method Man page Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed-method Man page Man page
makePdInfoPackage,AffySNPPDInfoPkgSeed2-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
mpsParser Source code
msgBar Source code
msgOK Source code
msgParsingFile Source code
parseAnnotFile Source code
parseBpmapCel Source code
parseCdfCelProbe Source code
parseCdfSeqAnnot Source code
parseCdfSeqAnnotSnp Source code
parseHtaProbesetCSV Source code
parseNgsPair Source code
parseNgsTrio Source code
parsePgfClf Source code
parseProbeSequenceFile Source code
parseProbesetCSV Source code
pmmmBlockToMat Source code
printTime Source code
probesetIdxToAtomIdx Source code
probesetIdxToTripletIdx Source code
readCdfUnitToMat Source code
readCdfUnitToMat.affyExpr Source code
readCdfUnitToMat.affyTiling Source code
readCdfUnitToMat.affyTiling2 Source code
readCdfUnitToMat.cnv Source code
readCdfUnitToMat.cnv.old Source code
seqToMat Source code
sequenceParser Man page Source code
setupPackage Source code
simpleMessage Source code
snp6.buildPdInfoDb Source code
snp6.createFeatureTableInfo Source code
snp6.createIndicesDb Source code
snp6.createTableInfoTable Source code
snp6.initDb Source code
snp6.loadAffyCsv Source code
snp6.loadAffyCsv.cnv Source code
snp6.loadAffySeqCsv Source code
snp6.loadAffySeqCsv.cnv Source code
snp6.loadUnitNames Source code
snp6.loadUnitNames.cnv Source code
snp6.loadUnits.cnv Source code
snp6.loadUnits.snp Source code
snp6.loadUnitsByBatch Source code
snp6.sortFeatureTables Source code
sortFeatureTables Source code
validInput Source code

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
pdInfoBuilder documentation built on May 20, 2017, 9:41 p.m.