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Accompanying documentation is available in the subdirectory "doc" of the installed package.

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

-- A --

ABPkgBuilder Functions that support a single API for building data packages
AnnInfo A text file containing annotaion data information

-- B --

baseFile Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

-- C --

cols2Env Creates a environment object using data from two columns of a matrix
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

-- 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
findNumCol Functions to get/process yeast genome data
findYGChrLength Functions to do a data package for yeast genome
formatABQCList A function 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

-- 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
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
getChroLocation Functions to extract data from golden path
getDate A function to read in the statistics about a data package
getDirContent Functions that support a single API for building data packages
getDPStats A function 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
getExample Functions that write supporting files needed by a data package
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
getGOUrl Functions that find the correct url for downloading annotation data
getGPData Functions to extract data from golden path
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
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
getLLBuilt Functions that get the built date or number of the source data used for annotation
getLLPathMap Functions to get/process pathway and enzyme data from KEGG
getLLUrl Functions that find the correct url for downloading annotation data
getMultiColNames Functions that support a single API for building data packages
getNoDup Functions to obtain unified mappings between ids
getOffspringNodes Functions to read/parse the XML document of Gene Ontology data
getParentNodes Functions to read/parse the XML document of Gene Ontology data
getPBased A function to read in the statistics about a data package
getProbe2SGD Functions to annotate yeast genom data
getProbeNum A function to read in the statistics about a data package
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
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
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
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 between ids
getUrlNBuilt Functions that write supporting files needed by a data package
getVote Functions to obtain unified mappings between ids
getYeastData Functions to get/process yeast genome data
getYGBuilt Functions that get the built date or number of the source data used for annotation
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 A functions to builder 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 between ids

-- K --

KEGG 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

-- 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
mapGO2AllProbe Functions to read/parse the XML document of Gene Ontology data
mapGO2Category Functions to read/parse the XML document of Gene Ontology data
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
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 A function to read in the statistics about a data package
mergeRowByKey Dynamically create a Perl script to parse a source file base on user specifications

-- O --

organism Class "UG" a sub-class of pubRepo to handle data from UniGene

-- P --

parseData 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
parser 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
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 --

readBadData Functions to get/process yeast genome data
readData Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories
readURL Functions that find the correct url for downloading annotation data
resolveMaps Functions to obtain unified mappings between ids

-- S --

sourceURLs A data file contains urls for data available from various public repositories
splitEntry Functions that support a single API for building data packages
srcUrl 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
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

-- W --

writeAccessory Functions that write supporting files needed by a data package
writeChrLength Functions that creates binary files for chromosome length and organism
writeDescription Functions that write supporting files needed by a data package
writeFun Functions that write supporting files needed by a 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
writeREADME Functions that write supporting files needed by a data package
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