Entry: ABPkgBuilder
Aliases: ABPkgBuilder getBaseParsers createEmptyDPkg getDirContent getMultiColNames getUniColNames getTypeColNames splitEntry twoStepSplit saveMat saveList getChrLenghts nameGOByCat getChrLengths getHumanChrLengths getMouseChrLengths getRatChrLengths getYeastChrLengths getList4GO vect2List resumeSrcUrl writeDatalist getEGAccName
Keywords: manip
Description: Functions that support a single API for building data packages
URL: ../../../library/AnnBuilder/html/ABPkgBuilder.html

Entry: EG-class
Aliases: EG-class parseData,EG-method EG
Keywords: classes
Description: Class "EG" handles data provided by Entrez Gene
URL: ../../../library/AnnBuilder/html/EG-class.html

Entry: GEO-class
Aliases: GEO-class GEO readData,GEO-method
Keywords: classes
Description: Class "GEO" represents a GEO object that reads/downloads data from the GEO web site
URL: ../../../library/AnnBuilder/html/GEO-class.html

Entry: GO-class
Aliases: GO-class GO readData,GO-method
Keywords: classes
Description: Class "GO" a class to handle data from Gene Ontology
URL: ../../../library/AnnBuilder/html/GO-class.html

Entry: GOPkgBuilder
Aliases: GOPkgBuilder writeDocs copyTemplates getRepList
Keywords: manip
Description: Functions to build a data package using GO data
URL: ../../../library/AnnBuilder/html/GOPkgBuilder.html

Entry: GOXMLParser
Aliases: GOXMLParser
Keywords: manip
Description: Parse the Gene Ontology OBO XML data file
URL: ../../../library/AnnBuilder/html/GOXMLParser.html

Entry: GP-class
Aliases: GP-class GP getStrand getStrand,GP-method
Keywords: classes
Description: Class "GP" a sub-class of pubRepo to get/process data from GoldenPath
URL: ../../../library/AnnBuilder/html/GP-class.html

Entry: HG-class
Aliases: HG-class HG readData,HG-method
Keywords: classes
Description: Class "HG" a class to represent HomoloGene data source
URL: ../../../library/AnnBuilder/html/HG-class.html

Entry: IPI-class
Aliases: IPI-class parseData,IPI-method IPI
Keywords: classes
Description: Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI)
URL: ../../../library/AnnBuilder/html/IPI-class.html

Entry: KEGG-class
Aliases: KEGG-class KEGG findIDNPath mapLL2ECNPName parseKEGGGenome KEGG,KEGG-method findIDNPath,KEGG-method mapLL2ECNPName,KEGG-method
Keywords: classes
Description: Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
URL: ../../../library/AnnBuilder/html/KEGG-class.html

Entry: KEGGPkgbuilder
Aliases: KEGGPkgBuilder getEIdNName getKEGGFile getKEGGGeneMap
Keywords: manip
Description: A function to make the data package for KEGG
URL: ../../../library/AnnBuilder/html/KEGGPkgBuilder.html

Entry: LL-class
Aliases: LL-class LL
Keywords: classes
Description: Class "LL" a sub-class of pubRepo to handle data from LocusLink
URL: ../../../library/AnnBuilder/html/LL-class.html

Entry: MeSHParser
Aliases: MeSHParser setVars
Keywords: manip
Description: Function to parse the XML data file form MeSH
URL: ../../../library/AnnBuilder/html/MeSHParser.html

Entry: PFAM-class
Aliases: PFAM-class parseData,PFAM-method PFAM
Keywords: classes
Description: Class "PFAM" a sub-class of pubRepo to handle data from http://www.sanger.ac.uk/Software/Pfam/
URL: ../../../library/AnnBuilder/html/PFAM-class.html

Entry: SPPkgBuilder
Aliases: SPPkgBuilder key getDetailV getEnvNames isOneToOne
Keywords: manip
Description: A function to build a data pckage using Swiss-Prot protein data
URL: ../../../library/AnnBuilder/html/SPPkgBuilder.html

Entry: UG-class
Aliases: UG-class orgName orgName<- orgName,UG-method orgName<-,UG-method UG
Keywords: classes
Description: Class "UG" a sub-class of pubRepo to handle data from UniGene
URL: ../../../library/AnnBuilder/html/UG-class.html

Entry: YEAST-class
Aliases: YEAST-class parseData,YEAST-method YEAST
Keywords: classes
Description: Class "YEAST" a sub-class of pubRepo to handle data from ftp.yeastgenome.org
URL: ../../../library/AnnBuilder/html/YEAST-class.html

Entry: YG-class
Aliases: YG-class YG readData,YG-method
Keywords: classes
Description: Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic
URL: ../../../library/AnnBuilder/html/YG-class.html

Entry: addNamespace
Aliases: addNamespace sealEnvs
Keywords: misc
Description: Functions to add namespaces for data files or seal the environment objects in the data subdirectory
URL: ../../../library/AnnBuilder/html/addNamespace.html

Entry: athPkgBuilder
Aliases: athPkgBuilder getOneMap procPMIDData getSrcObjs4Ath readAthData mergeDupMatByFirstCol getFileExt
Keywords: manip
Description: Functions that build annotation packages for Arbidopsis
URL: ../../../library/AnnBuilder/html/athPkgBuilder.html

Entry: cMapPathBuilder
Aliases: cMapPathBuilder cMAPParser
Keywords: manip
Description: Functions that build a data pacakge using data provided by cMAP
URL: ../../../library/AnnBuilder/html/cMapPathBuilder.html

Entry: chrLocPkgBuilder
Aliases: chrLocPkgBuilder getChrNum saveCytoband getChroms4Org
Keywords: manip
Description: A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids
URL: ../../../library/AnnBuilder/html/chrLocPkgBuilder.html

Entry: cleanSrcObjs
Aliases: cleanSrcObjs getRepSourceNBuilt mapGO2Probe writeReverseMap writeAnnData2Pkg getAnnData getUniMappings getBaseFile getSrcObjs mapll2PathID mapLLNGB getLLNGBMap getRepList4Perl mapUGNGB getTaxid
Keywords: misc
Description: Supporting function that may no of any other usese
URL: ../../../library/AnnBuilder/html/cleanSrcObjs.html

Entry: cols2Env
Aliases: cols2Env matchAll matchOneRow
Keywords: manip
Description: Creates a environment object using data from two columns of a matrix
URL: ../../../library/AnnBuilder/html/cols2Env.html

Entry: descriptionInfo
Aliases: descriptionInfo biocPkgNameIndex biocViewsIndex manufacturerIndex organismIndex
Keywords: datasets
Description: Detailed DESCRIPTION Information
URL: ../../../library/AnnBuilder/html/descriptionInfo.html

Entry: downloadSourceData
Aliases: downloadSourceData
Keywords: data
Description: Create a local mirror of annotation data sources
URL: ../../../library/AnnBuilder/html/downloadSourceData.html

Entry: fileMuncher
Aliases: fileMuncher mergeRowByKey
Keywords: manip
Description: Dynamically create a Perl script to parse a source file base on user specifications
URL: ../../../library/AnnBuilder/html/fileMuncher.html

Entry: fileToXML
Aliases: fileToXML
Keywords: manip
Description: A function to convert a text file to XML.
URL: ../../../library/AnnBuilder/html/fileToXML.html

Entry: getChroLocation
Aliases: getChroLocation getGPData gpLinkNGene getCytoList getCytoLoc
Keywords: manip
Description: Functions to extract data from Golden Path
URL: ../../../library/AnnBuilder/html/getChroLocation.html

Entry: getDPStats
Aliases: getDPStats getDate getProbeNum matchProbes getPBased formatABQCList countMapping
Keywords: misc
Description: Functions to read in the statistics about a data package
URL: ../../../library/AnnBuilder/html/getDPStats.html

Entry: getKEGGIDNName
Aliases: getKEGGIDNName getKEGGOrgName getLLPathMap mapll2EC parseEC
Keywords: manip
Description: Functions to get/process pathway and enzyme data from KEGG
URL: ../../../library/AnnBuilder/html/getKEGGIDNName.html

Entry: getPubDataGo
Aliases: getPubDataHomoloGene getPubDataLocusLink getPubDataUniGene getPubDataEntrezGene getPubDataGoldenPath getPubDataGo getPubDataYeastGenome getPubDataKegg
Keywords: data
Description: Functions to download public domain annotation data sources
URL: ../../../library/AnnBuilder/html/getPubDataGo.html

Entry: getSrcBuilt
Aliases: getSrcBuilt getLLBuilt getUGBuilt getUCSCBuilt getGOBuilt getKEGGBuilt getYGBuilt getHGBuilt getRefBuilt4HS getRefSeqBuilt getEGBuilt
Keywords: datasets
Description: Functions that get the built date or number of the source data used for annotation
URL: ../../../library/AnnBuilder/html/getSrcBuilt.html

Entry: getSrcUrl
Aliases: getSrcUrl getAllUrl getLLUrl getUGUrl getUCSCUrl getGOUrl getKEGGUrl readURL getGEOUrl getYGUrl getHGUrl getRefSeqUrl getEGUrl
Keywords: datasets
Description: Functions that find the correct url for downloading annotation data
URL: ../../../library/AnnBuilder/html/getSrcUrl.html

Entry: getUGShortName
Aliases: getUGShortName UGSciNames getShortSciName
Keywords: misc
Description: Functions that produce short versions of organism names used by UniGene or for other purposes
URL: ../../../library/AnnBuilder/html/getUGShortName.html

Entry: getYeastData
Aliases: getYeastData readBadData findNumCol
Keywords: manip
Description: Functions to get/process yeast genome data
URL: ../../../library/AnnBuilder/html/getYeastData.html

Entry: homoPkgBuilder
Aliases: homoPkgBuilder procHomoData getLL2IntID getIntIDMapping mapIntID writeRdaNMan mapPS getHomoPS getHomoDList getHomoData getHomoData saveOrgNameNCode HomoData2List
Keywords: manip
Description: Functions to build a homology data package using data from NCBI
URL: ../../../library/AnnBuilder/html/homoPkgBuilder.html

Entry: loadFromUrl
Aliases: loadFromUrl validateUrl unzipFile
Keywords: manip
Description: Functions to load files from a web site
URL: ../../../library/AnnBuilder/html/loadFromUrl.html

Entry: makeLLDB
Aliases: makeLLDB
Keywords: manip
Description: Create a lazy loading database for package data files
URL: ../../../library/AnnBuilder/html/makeLLDB.html

Entry: makeSrcInfo
Aliases: makeSrcInfo getAllSrc
Keywords: file
Description: Functions to make source information available for later use
URL: ../../../library/AnnBuilder/html/makeSrcInfo.html

Entry: map2LL
Aliases: map2LL getExten saveColSepData getOrgName getReverseMapping saveData2Env reverseMap4GO getLL2ACC
Keywords: manip
Description: A function that maps LocusLink ids to other public repository ids and vice versa
URL: ../../../library/AnnBuilder/html/map2LL.html

Entry: pfamBuilder
Aliases: pfamBuilder
Keywords: manip
Description: Building Functions for the Data Package of Pfam Database
URL: ../../../library/AnnBuilder/html/pfamBuilder.html

Entry: print.ABQCList
Aliases: print.ABQCList
Keywords: misc
Description: Prints the quality control results for a given data package in a nice format
URL: ../../../library/AnnBuilder/html/print.ABQCList.html

Entry: pubDataURLs
Aliases: pubDataURLs
Keywords: datasets
Description: Public Domain Data Source URLs
URL: ../../../library/AnnBuilder/html/pubDataURLs.html

Entry: pubRepo-class
Aliases: pubRepo-class baseFile<- baseFile builtInfo downloadData parseData parser<- parser readData srcUrl<- srcUrl baseFile<-,pubRepo-method baseFile,pubRepo-method downloadData,pubRepo-method parseData,pubRepo-method parser<-,pubRepo-method fromWeb<-,pubRepo-method parser,pubRepo-method readData,pubRepo-method srcUrl<-,pubRepo-method srcUrl,pubRepo-method builtInfo,pubRepo-method pubRepo fromWeb fromWeb<- fromWeb,pubRepo-method
Keywords: classes
Description: Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
URL: ../../../library/AnnBuilder/html/pubRepo-class.html

Entry: queryGEO
Aliases: queryGEO
Keywords: manip
Description: Function to extract a data file from the GEO web site
URL: ../../../library/AnnBuilder/html/queryGEO.html

Entry: readSourceUrlConfig
Aliases: readSourceUrlConfig
Keywords: data
Description: Read a data source URL config file
URL: ../../../library/AnnBuilder/html/readSourceUrlConfig.html

Entry: resolveMaps
Aliases: resolveMaps getVote hasDelimit getUnified getNoDup
Keywords: manip
Description: Functions to obtain unified mappings for a given set of ids using various sources
URL: ../../../library/AnnBuilder/html/resolveMaps.html

Entry: sourceURLs
Aliases: sourceURLs
Keywords: file
Description: A data file contains urls for data available from various public repositories
URL: ../../../library/AnnBuilder/html/sourceURLs.html

Entry: unifyMappings
Aliases: unifyMappings
Keywords: manip
Description: A function to unify mapping result from different sources
URL: ../../../library/AnnBuilder/html/unifyMappings.html

Entry: wget
Aliases: wget
Keywords: data
Description: Wrapper for system wget
URL: ../../../library/AnnBuilder/html/wget.html

Entry: writeChrLength
Aliases: writeChrLength findChrLength writeOrganism
Keywords: manip
Description: Functions that creates binary files for chromosome length and organism
URL: ../../../library/AnnBuilder/html/writeChrLength.html

Entry: writeHomoXMLData
Aliases: writeHomoXMLData writeHGID2Caption writeHGID2LL writeHomoData homoXMLParser
Keywords: manip
Description: Functions to parse HomoloGene XML data file and build the homology annotation data package
URL: ../../../library/AnnBuilder/html/writeHomoXMLData.html

Entry: writeManPage
Aliases: writeManPage writeMan4Fun formatName writeREADME writeDescription getDsrc getItem getSrcNBuilt getUrlNBuilt getDSrc writeAccessory writeZZZ getAllRdaName writeFun escapeLatexChr writeMan4QC getExample getSrcBuiltNRef getBuild4Yeast
Keywords: manip
Description: Functions that write supporting files needed by a data package
URL: ../../../library/AnnBuilder/html/writeManPage.html

Entry: writeSourceUrlConfig
Aliases: writeSourceUrlConfig
Keywords: data
Description: Create a source URL config file
URL: ../../../library/AnnBuilder/html/writeSourceUrlConfig.html

Entry: writeXMLHeader
Aliases: writeXMLHeader
Keywords: manip
Description: A function to write header information to an XML file.
URL: ../../../library/AnnBuilder/html/writeXMLHeader.html

Entry: yeastAnn
Aliases: yeastAnn getProbe2SGD procYeastGeno formatGO formatChrLoc getGEOYeast getYGExons
Keywords: manip
Description: Functions to annotate yeast genom data
URL: ../../../library/AnnBuilder/html/yeastAnn.html

Entry: yeastPkgBuilder
Aliases: yeastPkgBuilder findYGChrLength
Keywords: manip
Description: Functions to do a data package for yeast genome
URL: ../../../library/AnnBuilder/html/yeastPkgBuilder.html
