Bioconductor annotation data package builder


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Documentation for package `AnnBuilder' version 1.4.21

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A B C D E F G H I K L M N O P Q R S T U V W Y

-- A --

ABPkgBuilder Functions that support a single API for building data packages
addNamespace Functions to add namespaces for data files or seal the environment objects in the data subdirectory
appendObsolete Functions to build a data package using GO data
athPkgBuilder Functions that build annotation packages for Arbidopsis

-- B --

baseFile Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
baseFile,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
baseFile<-,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
builtInfo Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
builtInfo,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- C --

chrLocPkgBuilder A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids
cleanSrcObjs Supporting function that may no of any other usese
cMAPParser Functions that build a data pacakge using data provided by cMAP
cMapPathBuilder Functions that build a data pacakge using data provided by cMAP
cols2Env Creates a environment object using data from two columns of a matrix
copyTemplates Functions to build a data package using GO data
countMapping Functions to read in the statistics about a data package
createEmptyDPkg Functions that support a single API for building data packages

-- D --

downloadData Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
downloadData,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- E --

escapeLatexChr Functions that write supporting files needed by a data package

-- F --

fileMuncher Dynamically create a Perl script to parse a source file base on user specifications
fileToXML A function to convert a text file to XML.
findChrLength Functions that creates binary files for chromosome length and organism
findIDNPath Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
findIDNPath,KEGG-method Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
findNumCol Functions to get/process yeast genome data
findYGChrLength Functions to do a data package for yeast genome
formatABQCList Functions to read in the statistics about a data package
formatChrLoc Functions to annotate yeast genom data
formatGO Functions to annotate yeast genom data
formatName Functions that write supporting files needed by a data package
fromWeb Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
fromWeb,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
fromWeb<-,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- G --

GEO Class "GEO" represents a GEO object that reads/downloads data from the GEO web site
GEO-class Class "GEO" represents a GEO object that reads/downloads data from the GEO web site
getAllRdaName Functions that write supporting files needed by a data package
getAllSrc Functions to make source information available for later use
getAllUrl Functions that find the correct url for downloading annotation data
getAncestors Functions to read/parse the XML document of Gene Ontology data
getAnnData Supporting function that may no of any other usese
getBaseFile Supporting function that may no of any other usese
getBaseParsers Functions that support a single API for building data packages
getBuild4Yeast Functions that write supporting files needed by a data package
getChildNodes Functions to read/parse the XML document of Gene Ontology data
getChrLenghts Functions that support a single API for building data packages
getChrLengths Functions that support a single API for building data packages
getChrNum A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids
getChroLocation Functions to extract data from Golden Path
getChroms4Org A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids
getCytoList Functions to extract data from Golden Path
getCytoLoc Functions to extract data from Golden Path
getDate Functions to read in the statistics about a data package
getDetailV A function to build a data pckage using Swiss-Prot protein data
getDirContent Functions that support a single API for building data packages
getDPStats Functions to read in the statistics about a data package
getDSrc Functions that write supporting files needed by a data package
getDsrc Functions that write supporting files needed by a data package
getEIdNName A function to make the data package for KEGG
getEnvNames A function to build a data pckage using Swiss-Prot protein data
getExample Functions that write supporting files needed by a data package
getExten A function that maps LocusLink ids to other public repository ids and vice versa
getGEOUrl Functions that find the correct url for downloading annotation data
getGEOYeast Functions to annotate yeast genom data
getGOBuilt Functions that get the built date or number of the source data used for annotation
getGOGroupIDs Functions to read/parse the XML document of Gene Ontology data
getGOTermsList Functions to build a data package using GO data
getGOUrl Functions that find the correct url for downloading annotation data
getGPData Functions to extract data from Golden Path
getHGBuilt Functions that get the built date or number of the source data used for annotation
getHGUrl Functions that find the correct url for downloading annotation data
getHomoData Functions to build a homology data package using data from NCBI
getHomoDList Functions to build a homology data package using data from NCBI
getHomoPS Functions to build a homology data package using data from NCBI
getHumanChrLengths Functions that support a single API for building data packages
getIntIDMapping Functions to build a homology data package using data from NCBI
getItem Functions that write supporting files needed by a data package
getKEGGBuilt Functions that get the built date or number of the source data used for annotation
getKEGGFile A function to make the data package for KEGG
getKEGGGeneMap A function to make the data package for KEGG
getKEGGIDNName Functions to get/process pathway and enzyme data from KEGG
getKEGGOrgName Functions to get/process pathway and enzyme data from KEGG
getKEGGUrl Functions that find the correct url for downloading annotation data
getList4GO Functions that support a single API for building data packages
getLL2ACC A function that maps LocusLink ids to other public repository ids and vice versa
getLL2IntID Functions to build a homology data package using data from NCBI
getLLBuilt Functions that get the built date or number of the source data used for annotation
getLLNGBMap Supporting function that may no of any other usese
getLLPathMap Functions to get/process pathway and enzyme data from KEGG
getLLUrl Functions that find the correct url for downloading annotation data
getMouseChrLengths Functions that support a single API for building data packages
getMultiColNames Functions that support a single API for building data packages
getNamedCat Functions that support a single API for building data packages
getNoDup Functions to obtain unified mappings for a given set of ids using various sources
getOffspringNodes Functions to read/parse the XML document of Gene Ontology data
getOneMap Functions that build annotation packages for Arbidopsis
getOrgName A function that maps LocusLink ids to other public repository ids and vice versa
getOrgNameNCode Functions to build a homology data package using data from NCBI
getParentNodes Functions to read/parse the XML document of Gene Ontology data
getPBased Functions to read in the statistics about a data package
getProbe2SGD Functions to annotate yeast genom data
getProbeNum Functions to read in the statistics about a data package
getRatChrLengths Functions that support a single API for building data packages
getRefBuilt4HS Functions that get the built date or number of the source data used for annotation
getRefSeqBuilt Functions that get the built date or number of the source data used for annotation
getRefSeqUrl Functions that find the correct url for downloading annotation data
getRepList Functions to build a data package using GO data
getRepList4Perl Supporting function that may no of any other usese
getRepSourceNBuilt Supporting function that may no of any other usese
getReverseMapping A function that maps LocusLink ids to other public repository ids and vice versa
getShortSciName Functions that produce short versions of organism names used by UniGene or for other purposes
getSrcBuilt Functions that get the built date or number of the source data used for annotation
getSrcBuiltNRef Functions that write supporting files needed by a data package
getSrcNBuilt Functions that write supporting files needed by a data package
getSrcObjs Supporting function that may no of any other usese
getSrcObjs4Ath Functions that build annotation packages for Arbidopsis
getSrcUrl Functions that find the correct url for downloading annotation data
getStrand Class "GP" a sub-class of pubRepo to get/process data from GoldenPath
getStrand,GP-method Class "GP" a sub-class of pubRepo to get/process data from GoldenPath
getTopGOid Functions to read/parse the XML document of Gene Ontology data
getTypeColNames Functions that support a single API for building data packages
getUCSCBuilt Functions that get the built date or number of the source data used for annotation
getUCSCUrl Functions that find the correct url for downloading annotation data
getUGBuilt Functions that get the built date or number of the source data used for annotation
getUGShortName Functions that produce short versions of organism names used by UniGene or for other purposes
getUGUrl Functions that find the correct url for downloading annotation data
getUniColNames Functions that support a single API for building data packages
getUnified Functions to obtain unified mappings for a given set of ids using various sources
getUniMappings Supporting function that may no of any other usese
getUrlNBuilt Functions that write supporting files needed by a data package
getVote Functions to obtain unified mappings for a given set of ids using various sources
getYeastChrLengths Functions that support a single API for building data packages
getYeastData Functions to get/process yeast genome data
getYGBuilt Functions that get the built date or number of the source data used for annotation
getYGExons Functions to annotate yeast genom data
getYGUrl Functions that find the correct url for downloading annotation data
GO Class "GO" a class to handle data from Gene Ontology
GO-class Class "GO" a class to handle data from Gene Ontology
GOPkgBuilder Functions to build a data package using GO data
GOXMLParser Functions to read/parse the XML document of Gene Ontology data
GP Class "GP" a sub-class of pubRepo to get/process data from GoldenPath
GP-class Class "GP" a sub-class of pubRepo to get/process data from GoldenPath
gpLinkNGene Functions to extract data from Golden Path

-- H --

hasDelimit Functions to obtain unified mappings for a given set of ids using various sources
HG Class "HG" a class to represent HomoloGene data source
HG-class Class "HG" a class to represent HomoloGene data source
HomoData2List Functions to build a homology data package using data from NCBI
homoPkgBuilder Functions to build a homology data package using data from NCBI
homoXMLParser Functions to parse HomoloGene XML data file and build the homology annotation data package

-- I --

isOneToOne A function to build a data pckage using Swiss-Prot protein data

-- K --

KEGG Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
KEGG,KEGG-method Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
KEGG-class Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
KEGGPkgBuilder A function to make the data package for KEGG
key A function to build a data pckage using Swiss-Prot protein data

-- L --

LL Class "LL" a sub-class of pubRepo to handle data from LocusLink
LL-class Class "LL" a sub-class of pubRepo to handle data from LocusLink
loadFromUrl Functions to load files from a web site

-- M --

makeSrcInfo Functions to make source information available for later use
map2LL A function that maps LocusLink ids to other public repository ids and vice versa
mapGO2AllProbe Functions to read/parse the XML document of Gene Ontology data
mapGO2Category Functions to read/parse the XML document of Gene Ontology data
mapGO2Probe Supporting function that may no of any other usese
mapIntID Functions to build a homology data package using data from NCBI
mapll2EC Functions to get/process pathway and enzyme data from KEGG
mapLL2ECNPName Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
mapLL2ECNPName,KEGG-method Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
mapll2PathID Supporting function that may no of any other usese
mapLLNGB Supporting function that may no of any other usese
mapOrgs Functions to build a homology data package using data from NCBI
mapPS Functions to build a homology data package using data from NCBI
mapUGNGB Supporting function that may no of any other usese
matchAll Creates a environment object using data from two columns of a matrix
matchOneRow Creates a environment object using data from two columns of a matrix
matchProbes Functions to read in the statistics about a data package
mergeDupMatByFirstCol Functions that build annotation packages for Arbidopsis
mergeRowByKey Dynamically create a Perl script to parse a source file base on user specifications
MeSHParser Function to parse the XML data file form MeSH

-- N --

nameGOByCat Functions that support a single API for building data packages

-- O --

orgName Class "UG" a sub-class of pubRepo to handle data from UniGene
orgName,UG-method Class "UG" a sub-class of pubRepo to handle data from UniGene
orgName<-,UG-method Class "UG" a sub-class of pubRepo to handle data from UniGene
orgNameNCode Functions to build a homology data package using data from NCBI

-- P --

parseData Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
parseData,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
parseEC Functions to get/process pathway and enzyme data from KEGG
parseKEGGGenome Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information
parser Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
parser,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
parser<-,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
print.ABQCList Prints the quality control results for a given data package in a nice format
procHomoData Functions to build a homology data package using data from NCBI
procPMIDData Functions that build annotation packages for Arbidopsis
procYeastGeno Functions to annotate yeast genom data
pubRepo Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
pubRepo-class Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- Q --

queryGEO Function to extract a data file from the GEO web site

-- R --

readAthData Functions that build annotation packages for Arbidopsis
readBadData Functions to get/process yeast genome data
readData Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
readData,GEO-method Class "GEO" represents a GEO object that reads/downloads data from the GEO web site
readData,GO-method Class "GO" a class to handle data from Gene Ontology
readData,HG-method Class "HG" a class to represent HomoloGene data source
readData,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
readData,YG-method Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic
readURL Functions that find the correct url for downloading annotation data
resolveMaps Functions to obtain unified mappings for a given set of ids using various sources
resumeSrcUrl Functions that support a single API for building data packages
reverseMap4GO A function that maps LocusLink ids to other public repository ids and vice versa

-- S --

saveColSepData A function that maps LocusLink ids to other public repository ids and vice versa
saveCytoband A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids
saveData2Env A function that maps LocusLink ids to other public repository ids and vice versa
saveList Functions that support a single API for building data packages
saveMat Functions that support a single API for building data packages
saveOrgNameNCode Functions to build a homology data package using data from NCBI
sealEnvs Functions to add namespaces for data files or seal the environment objects in the data subdirectory
setVars Function to parse the XML data file form MeSH
sourceURLs A data file contains urls for data available from various public repositories
splitEntry Functions that support a single API for building data packages
SPPkgBuilder A function to build a data pckage using Swiss-Prot protein data
srcUrl Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
srcUrl,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
srcUrl<-,pubRepo-method Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- T --

twoStepSplit Functions that support a single API for building data packages

-- U --

UG Class "UG" a sub-class of pubRepo to handle data from UniGene
UG-class Class "UG" a sub-class of pubRepo to handle data from UniGene
UGSciNames Functions that produce short versions of organism names used by UniGene or for other purposes
unifyMappings A function to unify mapping result from different sources
unzipFile Functions to load files from a web site

-- V --

validateUrl Functions to load files from a web site
vect2List Functions that support a single API for building data packages

-- W --

writeAccessory Functions that write supporting files needed by a data package
writeAnnData2Pkg Supporting function that may no of any other usese
writeChrLength Functions that creates binary files for chromosome length and organism
writeDatalist Functions that support a single API for building data packages
writeDescription Functions that write supporting files needed by a data package
writeDocs Functions to build a data package using GO data
writeFun Functions that write supporting files needed by a data package
writeHGID2Caption Functions to parse HomoloGene XML data file and build the homology annotation data package
writeHGID2LL Functions to parse HomoloGene XML data file and build the homology annotation data package
writeHomoData Functions to parse HomoloGene XML data file and build the homology annotation data package
writeHomoXMLData Functions to parse HomoloGene XML data file and build the homology annotation data package
writeMan4Fun Functions that write supporting files needed by a data package
writeMan4QC Functions that write supporting files needed by a data package
writeManPage Functions that write supporting files needed by a data package
writeOrganism Functions that creates binary files for chromosome length and organism
writeRdaNMan Functions to build a homology data package using data from NCBI
writeREADME Functions that write supporting files needed by a data package
writeReverseMap Supporting function that may no of any other usese
writeXMLHeader A function to write header information to an XML file.
writeZZZ Functions that write supporting files needed by a data package

-- Y --

yeastAnn Functions to annotate yeast genom data
yeastPkgBuilder Functions to do a data package for yeast genome
YG Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic
YG-class Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic