# Protein annotation data package builder

## Documentation for package ‘PAnnBuilder’ version 1.32.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C D F G H I L M O P S T U V W misc

## -- B --

bfBuilder_DB | Build Data Packages for Body Fluid Proteomes

## -- C --

copyTemplates | Write Help Documents
copyTemplates_DB | Write Help Documents
createAnnObjs | Creates the AnnObj instances
createEmptyDPkg | Parse and Write Data into R Data Packages
createSeeds | Creates the AnnObj instances
crossBuilder_DB | Build Data Packages for Protein ID Mapping

## -- D --

dbschema | Creates the AnnObj instances
dbschema-method | Creates the AnnObj instances
descriptionInfo | Load packages and data
dNameBuilder_DB | Build Data Packages for Mapping between ID and Name

## -- F --

fasta2list | Build Data Packages for Protein ID Mapping
fileMuncher | Convert Data Format
fileMuncher_DB | Convert Data Format

## -- G --

get3DIDBuilt | Get the Url and Release information for Diverse Databases
get3DIDUrl | Get the Url and Release information for Diverse Databases
getALLBuilt | Get the Url and Release information for Diverse Databases
getALLUrl | Get the Url and Release information for Diverse Databases
getBACELLOBuilt | Get the Url and Release information for Diverse Databases
getBACELLOUrl | Get the Url and Release information for Diverse Databases
getBaseData | Convert Data Format
getBaseParsers | Convert Data Format
getDBSUBLOCBuilt | Get the Url and Release information for Diverse Databases
getDBSUBLOCUrl | Get the Url and Release information for Diverse Databases
getDOMINEBuilt | Get the Url and Release information for Diverse Databases
getDOMINEUrl | Get the Url and Release information for Diverse Databases
getGENEINTBuilt | Get the Url and Release information for Diverse Databases
getGENEINTUrl | Get the Url and Release information for Diverse Databases
getGOABuilt | Get the Url and Release information for Diverse Databases
getGOAUrl | Get the Url and Release information for Diverse Databases
getGOUrl | Get the Url and Release information for Diverse Databases
getHOMOLOGENEBuilt | Get the Url and Release information for Diverse Databases
getHOMOLOGENEUrl | Get the Url and Release information for Diverse Databases
getINPARANOIDBuilt | Get the Url and Release information for Diverse Databases
getINPARANOIDUrl | Get the Url and Release information for Diverse Databases
getINTACTBuilt | Get the Url and Release information for Diverse Databases
getINTACTUrl | Get the Url and Release information for Diverse Databases
getINTERPROBuilt | Get the Url and Release information for Diverse Databases
getINTERPROUrl | Get the Url and Release information for Diverse Databases
getIPIBuilt | Get the Url and Release information for Diverse Databases
getIPISQUrl | Get the Url and Release information for Diverse Databases
getIPIUrl | Get the Url and Release information for Diverse Databases
getKEGGUrl | Get the Url and Release information for Diverse Databases
getMPPIBuilt | Get the Url and Release information for Diverse Databases
getMPPIUrl | Get the Url and Release information for Diverse Databases
getPEPTIDEATLASBuilt | Get the Url and Release information for Diverse Databases
getPEPTIDEATLASUrl | Get the Url and Release information for Diverse Databases
getPFAMBuilt | Get the Url and Release information for Diverse Databases
getPFAMUrl | Get the Url and Release information for Diverse Databases
getPROSITENAMEBuilt | Get the Url and Release information for Diverse Databases
getPROSITENAMEUrl | Get the Url and Release information for Diverse Databases
getREFSEQBuilt | Get the Url and Release information for Diverse Databases
getREFSEQSQUrl | Get the Url and Release information for Diverse Databases
getREFSEQUrl | Get the Url and Release information for Diverse Databases
getRepList | Write Help Documents
getSCOPBuilt | Get the Url and Release information for Diverse Databases
getSCOPUrl | Get the Url and Release information for Diverse Databases
getShortSciName | Get the Url and Release information for Diverse Databases
getSPBuilt | Get the Url and Release information for Diverse Databases
getSPUrl | Get the Url and Release information for Diverse Databases
getSrcBuilt | Get the Url and Release information for Diverse Databases
getSrcObjs | Convert Data Format
getSrcSQBuilt | Get the Url and Release information for Diverse Databases
getSrcSQUrl | Get the Url and Release information for Diverse Databases
getSrcUrl | Get the Url and Release information for Diverse Databases
getSYSBODYFLUIDBuilt | Get the Url and Release information for Diverse Databases
getSYSBODYFLUIDUrl | Get the Url and Release information for Diverse Databases
getSYSPTMBuilt | Get the Url and Release information for Diverse Databases
getSYSPTMUrl | Get the Url and Release information for Diverse Databases
getTREMBLBuilt | Get the Url and Release information for Diverse Databases
getTREMBLUrl | Get the Url and Release information for Diverse Databases
GOABuilder_DB | Build Data Packages for Proteomics Gene Ontology

## -- H --

HomoloGeneBuilder_DB | Build Data Packages for Homolog Protein Group

## -- I --

idBlast | Build Data Packages for Protein ID Mapping
InParanoidBuilder_DB | Build Data Packages for Ortholog Protein Group
intBuilder_DB | Build Data Package for Interaction

## -- L --

loadFromUrl | Load Files from a Web Site

## -- M --

makeLLDB | Create a Lazy Loading Database for Package Data Files
mergeRowByKey | Convert Data Format

## -- O --

organism2alias | Get the Url and Release information for Diverse Databases
organism2species | Get the Url and Release information for Diverse Databases
organism2taxID | Get the Url and Release information for Diverse Databases

## -- P --

pBase | Define Class and Object
pBaseBuilder_DB | Build Data Packages for Primary Protein Database
PeptideAtlasBuilder_DB | Build data package for experimentally identified peptides
processData | Convert Data Format
pSeqBuilder_DB | Build Data Packages for Query Sequences
ptmBuilder_DB | Build Data Packages for Protein Post-Translational Modifications

## -- S --

scopBuilder_DB | Build Data Package for Structural Classification of Proteins
sourceURLs | Load packages and data
speciesNorganism | Get the Url and Release information for Diverse Databases
splitEntry | Convert Data Format
subcellBuilder_DB | Build Data Package for Protein Subcellular Location

## -- T --

taxID2organism | Get the Url and Release information for Diverse Databases
taxLists | Load packages and data
twoStepSplit | Convert Data Format

## -- U --

unzipFile | Load Files from a Web Site

## -- V --

validateUrl | Load Files from a Web Site

## -- W --

write3DIDData_DB | Parse and Write Data into R Data Packages
writeBACELLOData_DB | Parse and Write Data into R Data Packages
writeData_DB | Parse and Write Data into R Data Packages
writeDBSUBLOCData_DB | Parse and Write Data into R Data Packages
writeDescription | Write Help Documents
writeDescription_DB | Write Help Documents
writeDOMINEData_DB | Parse and Write Data into R Data Packages
writeGENEINTData_DB | Parse and Write Data into R Data Packages
writeGOAData_DB | Parse and Write Data into R Data Packages
writeGOName_DB | Parse and Write Data into R Data Packages
writeHomoloGeneData_DB | Parse and Write Data into R Data Packages
writeInParanoidData_DB | Parse and Write Data into R Data Packages
writeInput | Convert Data Format
writeInputBLAST | Convert Data Format
writeInputINTERPRO | Convert Data Format
writeInputIPI | Convert Data Format
writeInputPFAM | Convert Data Format
writeInputREFSEQ | Convert Data Format
writeInputSP | Convert Data Format
writeINTACTData_DB | Parse and Write Data into R Data Packages
writeINTERPROName_DB | Parse and Write Data into R Data Packages
writeIPIData_DB | Parse and Write Data into R Data Packages
writeKEGGName_DB | Parse and Write Data into R Data Packages
writeManAnno | Write Help Documents
writeManAnno_DB | Write Help Documents
writeManMerge | Write Help Documents
writeManSQ | Write Help Documents
writeMeta_DB | Parse and Write Data into R Data Packages
writeMPPIData_DB | Parse and Write Data into R Data Packages
writeName_DB | Parse and Write Data into R Data Packages
writeOutput | Convert Data Format
writePeptideAtlasData_DB | Parse and Write Data into R Data Packages
writePFAMName_DB | Parse and Write Data into R Data Packages
writeREFSEQData_DB | Parse and Write Data into R Data Packages
writeSCOPData_DB | Parse and Write Data into R Data Packages
writeSPData_DB | Parse and Write Data into R Data Packages
writeSYSBODYFLUIDData_DB | Parse and Write Data into R Data Packages
writeSYSPTMData_DB | Parse and Write Data into R Data Packages
writeTAXName_DB | Parse and Write Data into R Data Packages

## -- misc --

.callPerl | Convert Data Format
.onLoad | Load packages and data
.srcUrls | Get the Url and Release information for Diverse Databases