# Annotation for microarrays

## Documentation for package `annotate' version 1.10.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D 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,pubMedAbst-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstUrl | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstUrl,pubMedAbst-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
ACC2homology | 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
articleTitle | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
articleTitle,pubMedAbst-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,pubMedAbst-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

## -- B --

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 LocusLink id
chromInfo | Class chromLocation, a class for describing genes and their chromosome mappings.
chromInfo,chromLocation-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,chromLocation-method | 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,chromLocation-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,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
compatibleVersions | function to check to see if the packages represented by the names passed have the same version number

## -- D --

dataSource | Class chromLocation, a class for describing genes and their chromosome mappings.
dataSource,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
Definition | Class "GOTerms"
Definition,GOTerms-method | Class "GOTerms"

## -- F --

fileName | Classes to represent HTML pages
fileName,HTMLPage-method | Classes to represent HTML pages
findChr4LL | A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
findNeighbors | A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
FramedHTMLPage | Classes to represent HTML pages
FramedHTMLPage,HTMLPage-method | Classes to represent HTML pages
FramedHTMLPage-class | Classes to represent HTML pages

## -- G --

genbank | A function to open the browser to Genbank with the selected gene.
genelocator | A function to identify genes by their LocusLink (or other id).
geneSymbols | Class chromLocation, a class for describing genes and their chromosome mappings.
geneSymbols,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
getBoundary | A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
getCells | Functions to create hypertext links that can be placed in a table cell of a HTML file
getGI | Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getGO | Functions to deal with Data Packages
getGOdesc | Functions to deal with Data Packages
getGPLNames | Function to extract data from the GEO web site
getLL | Functions to deal with Data Packages
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
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 | Functions to create hypertext links that can be placed in a table cell of a HTML file
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
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
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 LocusLink id
GO2heatmap | Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
GOID | Class "GOTerms"
GOID,GOTerms-method | Class "GOTerms"
GOmnplot | A function to plot by group means against each other.
GOTerms | Class "GOTerms"
GOTerms-class | Class "GOTerms"

## -- H --

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 | 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,homoData-method | Class "homoData"
homoData | Class "homoData"
homoData-class | Class "homoData"
homoHGID | Class "homoData"
homoHGID,homoData-method | Class "homoData"
homoLL | Class "homoData"
homoLL,homoData-method | Class "homoData"
homoOrg | Class "homoData"
homoOrg,homoData-method | Class "homoData"
homoPS | Class "homoData"
homoPS,homoData-method | Class "homoData"
homoType | Class "homoData"
homoType,homoData-method | Class "homoData"
homoURL | Class "homoData"
homoURL,homoData-method | Class "homoData"
HTMLPage | Classes to represent HTML pages
htmlpage | Functions to build HTML pages
HTMLPage,HTMLPage-method | Classes to represent HTML pages
HTMLPage-class | Classes to represent HTML pages

## -- I --

initialize,FramedHTMLPage-method | Classes to represent HTML pages
installDataPackage | A function to install data packages from the Internet

## -- J --

journal | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
journal,pubMedAbst-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.
KEGGmnplot | A function to plot by group means against each other.

## -- L --

LL2homology | Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
locuslinkByID | A function to open the browser to Locuslink with the selected gene.
locuslinkQuery | A function to open the browser to Locuslink using a provided search query.
lookUp | Functions to deal with Data Packages

## -- M --

mainPage | Classes to represent HTML pages
mainPage,FramedHTMLPage-method | Classes to represent HTML pages
mainPage,HTMLPage-method | Classes to represent HTML pages
makeAnchor | A Function To Generate HTML Anchors

## -- N --

nChrom | Class chromLocation, a class for describing genes and their chromosome mappings.
nChrom,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
neighborGeneFinder | A widget for locating genes neighboring a target gene

## -- O --

Ontology | Class "GOTerms"
Ontology,ANY-method | Class "GOTerms"
Ontology,GOTerms-method | Class "GOTerms"
organism | Class chromLocation, a class for describing genes and their chromosome mappings.
organism,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
orgNameNCode | Class "homoData"

## -- P --

p2LL | A function to map from probes to unique Entrez Gene IDs
pageText | Classes to represent HTML pages
pageText,HTMLPage-method | Classes to represent HTML pages
pageTitle | Classes to represent HTML pages
pageTitle,HTMLPage-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,pubMedAbst-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 | A function that does reverse the mappings between probe ids and the corresponding values
probesToChrom | Class chromLocation, a class for describing genes and their chromosome mappings.
probesToChrom,chromLocation-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,pubMedAbst-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,pubMedAbst-method | 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.
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
revBase | Functions to create anti-sense DNA string
revString | Functions to create anti-sense DNA string

## -- S --

Secondary | Class "GOTerms"
Secondary,GOTerms-method | Class "GOTerms"
serializeDataPkgEnvs | A Function To Serialize Environment
serializeEnv | A Function To Serialize Environment
show,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
show,FramedHTMLPage-method | Classes to represent HTML pages
show,GOTerms-method | Class "GOTerms"
show,homoData-method | Class "homoData"
show,HTMLPage-method | Classes to represent HTML pages
show,pubMedAbst-method | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
sidePage | Classes to represent HTML pages
sidePage,FramedHTMLPage-method | Classes to represent HTML pages
sidePage,HTMLPage-method | Classes to represent HTML pages
Synonym | Class "GOTerms"
Synonym,GOTerms-method | Class "GOTerms"

## -- T --

Term | Class "GOTerms"
Term,GOTerms-method | Class "GOTerms"
toFile | Classes to represent HTML pages
toFile,FramedHTMLPage-method | Classes to represent HTML pages
toFile,HTMLPage-method | Classes to represent HTML pages
topPage | Classes to represent HTML pages
topPage,FramedHTMLPage-method | Classes to represent HTML pages
topPage,HTMLPage-method | Classes to represent HTML pages

## -- U --

UniGeneQuery | Create a Query String for a UniGene Identifier
usedChromGenes | A function to select used genes on a chromosome from an exprSet.

## -- W --

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