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A B C D E F G H I K L M O P Q R S T U V W Y
| ABPkgBuilder | Functions that support a single API for building data packages |
| 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 |
| chrLocPkgBuilder | A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids |
| cols2Env | Creates a environment object using data from two columns of a matrix |
| createEmptyDPkg | Functions that support a single API for building data packages |
| 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 |
| escapeLatexChr | Functions that write supporting files needed by a data package |
| 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 | 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 |
| 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 |
| 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 |
| getDate | A function 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 | 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 |
| 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 |
| getFullIDName | 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 |
| 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 |
| getHomoPS | Functions to build a homology data package using data from NCBI |
| 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 |
| 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 |
| 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 |
| 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 |
| getOrgName | A function that maps LocusLink ids to other public repository ids and vice versa |
| 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 |
| getReverseMapping | A function that maps LocusLink ids to other public repository ids and vice versa |
| 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 |
| 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 |
| 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 |
| getUrl4Org | A function that maps LocusLink ids to other public repository ids and vice versa |
| 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 |
| hasDelimit | Functions to obtain unified mappings between ids |
| homoPkgBuilder | Functions to build a homology data package using data from NCBI |
| homoPS-class | Class "homoPS" |
| isOneToOne | A function to build a data pckage using Swiss-Prot protein data |
| 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 |
| 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 |
| 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 |
| 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 |
| mapOrgs | Functions to build a homology data package using data from NCBI |
| mapPS | Functions to build a homology data package using data from NCBI |
| 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 |
| organism | Class "UG" a sub-class of pubRepo to handle data from UniGene |
| organism,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
| organism<-,UG-method | Class "UG" a sub-class of pubRepo to handle data from UniGene |
| orgNameNCode | Class "homoPS" |
| 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 |
| 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 |
| procYeastGeno | Functions to annotate yeast genom data |
| ps | Class "homoPS" |
| ps,homoPS-method | Class "homoPS" |
| psLL | Class "homoPS" |
| psLL,homoPS-method | Class "homoPS" |
| psOrg | Class "homoPS" |
| psOrg,homoPS-method | Class "homoPS" |
| psType | Class "homoPS" |
| psType,homoPS-method | Class "homoPS" |
| psURL | Class "homoPS" |
| psURL,homoPS-method | Class "homoPS" |
| 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 |
| queryGEO | Function to extract a data file from the GEO web site |
| 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,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 between ids |
| reverseMap4GO | A function that maps LocusLink ids to other public repository ids and vice versa |
| saveColSepData | A function that maps LocusLink ids to other public repository ids and vice versa |
| saveData2Env | A function that maps LocusLink ids to other public repository ids and vice versa |
| 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 |
| twoStepSplit | Functions that support a single API for building data packages |
| 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 |
| validateUrl | Functions to load files from a web site |
| 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 |
| writeRdaNMan | Functions to build a homology data package using data from NCBI |
| 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 |
| 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 |