Entry: ABPkgBuilder
Aliases: ABPkgBuilder getBaseParsers createEmptyDPkg getDirContent getMultiColNames getUniColNames getTypeColNames splitEntry twoStepSplit
Keywords: manip
Description: Functions that support a single API for building data packages
URL: ../../../library/AnnBuilder/html/ABPkgBuilder.html

Entry: chrLocPkgBuilder
Aliases: chrLocPkgBuilder getChrNum
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: 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: 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: 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: getChroLocation
Aliases: getChroLocation getGPData gpLinkNGene
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
Keywords: misc
Description: A function 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: getSrcBuilt
Aliases: getSrcBuilt getLLBuilt getUGBuilt getUCSCBuilt getGOBuilt getKEGGBuilt getYGBuilt getHGBuilt
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
Keywords: datasets
Description: Functions that find the correct url for downloading annotation data
URL: ../../../library/AnnBuilder/html/getSrcUrl.html

Entry: getYeastData
Aliases: getYeastData readBadData findNumCol
Keywords: manip
Description: Functions to get/process yeast genome data
URL: ../../../library/AnnBuilder/html/getYeastData.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
Keywords: manip
Description: A functions to builder a data package using GO data
URL: ../../../library/AnnBuilder/html/GOPkgBuilder.html

Entry: GOXMLParser
Aliases: GOXMLParser getChildNodes getOffspringNodes getParentNodes getAncestors getTopGOid mapGO2Category getGOGroupIDs mapGO2AllProbe
Keywords: manip
Description: Functions to read/parse the XML document of Gene Ontology data
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: homoPkgBuilder
Aliases: homoPkgBuilder procHomoData getLL2IntID getIntIDMapping mapIntID mapOrgs writeRdaNMan mapPS getHomoPS
Keywords: manip
Description: Functions to build a homology data package using data from NCBI
URL: ../../../library/AnnBuilder/html/homoPkgBuilder.html

Entry: homoPS-class
Aliases: homoPS-class ps psLL psOrg psType psURL ps,homoPS-method psLL,homoPS-method psOrg,homoPS-method psType,homoPS-method psURL,homoPS-method orgNameNCode
Keywords: classes
Description: Class "homoPS"
URL: ../../../library/AnnBuilder/html/homoPS-class.html

Entry: KEGG-class
Aliases: KEGG-class KEGG findIDNPath mapLL2ECNPName 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
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: loadFromUrl
Aliases: loadFromUrl validateUrl unzipFile
Keywords: manip
Description: Functions to load files from a web site
URL: ../../../library/AnnBuilder/html/loadFromUrl.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 getUrl4Org getFullIDName saveData2Env reverseMap4GO
Keywords: manip
Description: A function that maps LocusLink ids to other public repository ids and vice versa
URL: ../../../library/AnnBuilder/html/map2LL.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: pubRepo-class
Aliases: pubRepo-class baseFile<- baseFile downloadData parseData parser<- parser readData srcUrl<- srcUrl baseFile<-,pubRepo-method baseFile,pubRepo-method downloadData,pubRepo-method parseData,pubRepo-method parser<-,pubRepo-method parser,pubRepo-method readData,pubRepo-method srcUrl<-,pubRepo-method srcUrl,pubRepo-method pubRepo
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: resolveMaps
Aliases: resolveMaps getVote hasDelimit getUnified getNoDup
Keywords: manip
Description: Functions to obtain unified mappings between ids
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: 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 organism organism<- organism,UG-method organism<-,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: unifyMappings
Aliases: unifyMappings
Keywords: manip
Description: A function to unify mapping result from different sources
URL: ../../../library/AnnBuilder/html/unifyMappings.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: 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: 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
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

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
