# Annotation for microarrays

## Documentation for package ‘annotate’ version 1.56.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- A --

abstText | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstText-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
ACC2homology | DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
accessionToUID | A function to convert accession values to NCBI UIDs.
ACCNUMStats | Provides statistics on the types of ids used for the ACCNUM environment of a given data package
allValidKeys | Get or verify valid IDs for a package.
annotate-defunct | Defunct Functions in Package 'annotate'
annPkgName | Get annotation package name from chip name
aqListGOIDs | List GO Identifiers by GO Ontology
articleTitle | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
articleTitle-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
authors | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
authors-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

## -- B --

blastSequences | Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.
buildChromLocation | A function to generate an instantiation of a chromLocation class
buildPubMedAbst | A function to generate an instantiation of a pubMedAbst class

## -- C --

checkArgs | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
chrCats | Returns a list of chromosome locations from a MAP environment
chromInfo | Class chromLocation, a class for describing genes and their chromosome mappings.
chromInfo-method | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLengths | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLengths-method | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocation | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocation-class | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocs | Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocs-method | Class chromLocation, a class for describing genes and their chromosome mappings.
chromNames | Class chromLocation, a class for describing genes and their chromosome mappings.
chromNames-method | Class chromLocation, a class for describing genes and their chromosome mappings.
clearRepository | Functions to add arbitrary repositories
compatibleVersions | function to check to see if the packages represented by the names passed have the same version number
createLLChrCats | Returns a list of chromosome locations from a MAP environment
createMAPIncMat | Returns a list of chromosome locations from a MAP environment

## -- D --

dataSource | Class chromLocation, a class for describing genes and their chromosome mappings.
dataSource-method | Class chromLocation, a class for describing genes and their chromosome mappings.
dropECode | Drop GO labels for specified Evidence Codes

## -- E --

entrezGeneByID | Create a Query String for an Entrez Gene Identifier
entrezGeneQuery | Create a Query String for Entrez Genes

## -- F --

fileName | Classes to represent HTML pages
fileName-method | Classes to represent HTML pages
filterGOByOntology | Filter GO terms by a specified GO ontology
findChr4LL | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
findNeighbors | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
FramedHTMLPage | Classes to represent HTML pages
FramedHTMLPage-class | Classes to represent HTML pages
FramedHTMLPage-method | Classes to represent HTML pages

## -- G --

genbank | A function to open the browser to Genbank with the selected gene.
genelocator | Defunct Functions in Package 'annotate'
geneSymbols | Class chromLocation, a class for describing genes and their chromosome mappings.
geneSymbols-method | Class chromLocation, a class for describing genes and their chromosome mappings.
getAnnMap | Get annotation map
getBoundary | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
getCells | Functions to create hypertext links that can be placed in a table cell of a HTML file
getEG | Functions to deal with Data Packages
getEvidence | Get the Evidence codes for a set of GO terms.
getGI | Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getGO | Functions to deal with Data Packages
getGOChildren | Functions to Access GO data.
getGOdesc | Functions to deal with Data Packages
getGOOntology | Functions to Access GO data.
getGOParents | Functions to Access GO data.
getGOTerm | Functions to Access GO data.
getGPLNames | Function to extract data from the GEO web site
getLL | Functions to deal with Data Packages
getOntology | Get GO terms for a specified ontology
getOrgNameNCode | Functions to map to organism IDs used by NCBI homology.
getPMID | Functions to deal with Data Packages
getPMInfo | extract publication details and abstract from annotate::pubmed function output
getQuery4Affy | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4EN | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4ENSEMBL | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4FB | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4GB | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4LL | Defunct Functions in Package 'annotate'
getQuery4OMIM | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4SP | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4TR | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4UG | Functions to create hypertext links that can be placed in a table cell of a HTML file
getQueryLink | Functions to create hypertext links that can be placed in a table cell of a HTML file
getRepositories | Functions to add arbitrary repositories
getSAGEFileInfo | Function to extract data from the GEO web site
getSAGEGPL | Function to extract data from the GEO web site
getSEQ | Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getSYMBOL | Functions to deal with Data Packages
getTDRows | Functions to create hypertext links that can be placed in a table cell of a HTML file
getUniqAnnItem | Functions to deal with Data Packages
getValidChr | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
GO2heatmap | Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
GOmnplot | A function to plot by group means against each other.

## -- H --

hasGOannote | Check for GO annotation
hgByChroms | A dataset to show the human genome base pair locations per chromosome.
hgCLengths | A dataset which contains the lengths (in base pairs) of the human chromosomes.
HGID2homology | DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
hgu95Achroloc | Annotation data for the Affymetrix HGU95A GeneChip
hgu95Achrom | Annotation data for the Affymetrix HGU95A GeneChip
hgu95All | Annotation data for the Affymetrix HGU95A GeneChip
hgu95AProbLocs | chromLocation instance hgu95AProbLocs, an example of a chromLocation object
hgu95Asym | Annotation data for the Affymetrix HGU95A GeneChip
homoACC | Class "homoData"
homoACC-method | Class "homoData"
homoData | Class "homoData"
homoData-class | Class "homoData"
homoHGID | Class "homoData"
homoHGID-method | Class "homoData"
homoLL | Class "homoData"
homoLL-method | Class "homoData"
homoOrg | Class "homoData"
homoOrg-method | Class "homoData"
homoPS | Class "homoData"
homoPS-method | Class "homoData"
homoType | Class "homoData"
homoType-method | Class "homoData"
homoURL | Class "homoData"
homoURL-method | Class "homoData"
HTMLPage | Classes to represent HTML pages
htmlpage | Functions to build HTML pages
HTMLPage-class | Classes to represent HTML pages
HTMLPage-method | Classes to represent HTML pages

## -- I --

initialize-method | Classes to represent HTML pages
isValidKey | Get or verify valid IDs for a package.

## -- J --

journal | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
journal-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

## -- K --

KEGG2heatmap | Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
KEGG2heatmap-method | Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
KEGGmnplot | A function to plot by group means against each other.
KEGGmnplot-method | A function to plot by group means against each other.

## -- L --

LL2homology | DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
lookUp | Functions to deal with Data Packages

## -- M --

mainPage | Classes to represent HTML pages
mainPage-method | Classes to represent HTML pages
makeAnchor | A Function To Generate HTML Anchors
mapOrgs | Functions to map to organism IDs used by NCBI homology.

## -- N --

nChrom | Class chromLocation, a class for describing genes and their chromosome mappings.
nChrom-method | Class chromLocation, a class for describing genes and their chromosome mappings.
neighborGeneFinder | Defunct Functions in Package 'annotate'

## -- O --

organism | Convenience function for getting the organism from an object or package
organism-method | Class chromLocation, a class for describing genes and their chromosome mappings.
organism-method | Convenience function for getting the organism from an object or package
orgNameNCode | Class "homoData"

## -- P --

p2LL | A function to map from probes to unique Entrez Gene IDs
pageText | Classes to represent HTML pages
pageText-method | Classes to represent HTML pages
pageTitle | Classes to represent HTML pages
pageTitle-method | Classes to represent HTML pages
pm.abstGrep | An interface to grep for PubMed abstracts.
pm.getabst | Obtain the abstracts for a set PubMed list.
pm.titles | Obtain the titles of the PubMed abstracts.
pmAbst2HTML | HTML Generation for PubMed Abstracts
pmid | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmid-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmid2MIAME | use web to populate MIAME instance with pubmed details
PMIDAmat | A function to compute the probe to PubMed id incidence matrix.
pmidQuery | A function to query PubMed
probesByLL | Defunct Functions in Package 'annotate'
probesToChrom | Class chromLocation, a class for describing genes and their chromosome mappings.
probesToChrom-method | Class chromLocation, a class for describing genes and their chromosome mappings.
pubDate | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubDate-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubmed | A function to open the browser to Pubmed with the selected gene.
pubMedAbst | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubMedAbst-class | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubMedAbst-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
PWAmat | A function to compute the probe to KEGG pathway incidence matrix.

## -- R --

readGEOAnn | Function to extract data from the GEO web site
readIDNAcc | Function to extract data from the GEO web site
readUrl | Function to extract data from the GEO web site

## -- S --

serializeDataPkgEnvs | A Function To Serialize Environment
serializeEnv | A Function To Serialize Environment
setRepository | Functions to add arbitrary repositories
show-method | Classes to represent HTML pages
show-method | Class chromLocation, a class for describing genes and their chromosome mappings.
show-method | Class "homoData"
show-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
sidePage | Classes to represent HTML pages
sidePage-method | Classes to represent HTML pages

## -- T --

toFile | Classes to represent HTML pages
toFile-method | Classes to represent HTML pages
topPage | Classes to represent HTML pages
topPage-method | Classes to represent HTML pages

## -- U --

UniGeneQuery | Create a Query String for a UniGene Identifier
updateSymbolsToValidKeys | Take a list of symbols and translate them into the best possible ID for a package.
usedChromGenes | A function to select used genes on a chromosome from an ExpressionSet.

## -- W --

weightByConfi | A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
whatACC | Provides statistics on the types of ids used for the ACCNUM environment of a given data package