# Annotation for microarrays

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D F G H I J L M N O P 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.
accessionToUID | A function to convert accession values to NCBI UIDs.
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.

## -- 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.

## -- 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
getGO | Functions to deal with Data Packages
getGOdesc | Functions to deal with Data Packages
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
getQuery4LL | 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
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

## -- 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.
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
HTMLPage | Classes to represent 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.

## -- L --

ll.htmlpage | Turn LocusLink ID's into a Clickable Web Page
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 --

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.

## -- P --

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.
pmidQuery | A function to query PubMed
probesByLL | A function that groups probe ids by LocusLink ids
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.

## -- S --

show,chromLocation-method | Class chromLocation, a class for describing genes and their chromosome mappings.
show,FramedHTMLPage-method | Classes to represent HTML pages
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

## -- T --

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