annaffy: Annotation tools for Affymetrix biological metadata

Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

AuthorColin A. Smith <>
Date of publicationNone
MaintainerColin A. Smith <>

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aaf.character: Generic constructor for classes extending character

aafChromLoc: Constructor for aafChromLoc objects

aafChromLoc-class: Class aafChromLoc, a class for gene chromosome locations

aafChromosome: Constructor for aafChromosome objects

aafChromosome-class: Class aafChromosome, a class for gene chromosome assignments

aafCytoband: Constructor for aafCytoband objects

aafCytoband-class: Class aafCytoband, a class for cytoband data

aafDescription: Constructor for aafDescription objects

aafDescription-class: Class aafDescription, a class for gene descriptions

aafExpr: Sample ExpressionSet used for demonstration purposes

aafGenBank: Constructor for aafGenBank objects

aafGenBank-class: Class aafGenBank, a class for GenBank accession numbers

aafGO: Constructor for aafGO objects

aafGO-class: Class aafGO, a class for gene ontology ids

aafGOItem-class: Class aafGOItem, a class for gene ontology id elements

aaf.goterm: Fetch Gene Ontology term information

aaf.handler: Handle feching annotation data columns

aaf.integer: Generic constructor for classes extending integer

aafIntensity-class: Class aafIntensity, a class for gene expression values

aafList-class: Class aafList, a specialized subclass of list

aafLocusLink: Constructor for aafLocusLink objects

aafLocusLink-class: Class aafLocusLink, a class for LocusLink ids

aafPathway: Constructor for aafPathway objects

aafPathway-class: Class aafPathway, a class for KEGG pathway ids

aafPathwayItem-class: Class aafPathwayItem, a class for KEGG pathway id elements

aafProbe: Constructor for aafProbe objects

aafProbe-class: Class aafProbe, a class for Probe ids

aafPubMed: Constructor for aafPubMed objects

aafPubMed-class: Class aafPubMed, a class for PubMed ids

aaf.raw: Fetch raw annotation data

aafSearchGO: Find probe ids corresponding to GO ids

aafSearchText: Search metadata annotation text

aafSigned-class: Class aafSigned, a class for signed numerical data

aafSymbol: Constructor for aafSymbol objects

aafSymbol-class: Class aafSymbol, a class for gene symbols

aafTable: Constructor for aafTable objects

aafTableAnn: Constructor for aafTable objects from annotation data

aafTable-class: Class aafTable, a tabular microarray data class

aafTableFrame: Constructor for aafTable objects from data frames

aafTableInt: Constructor for aafTable objects from ExpressionSets

aafUniGene: Constructor for aafUniGene objects

aafUniGene-class: Class aafUniGene, a class for UniGene cluster ids

chkPkgs: A Function to Check for and Install Missing Annotation...

getCSS-methods: Methods for function getCSS

getHTML-methods: Methods for function getHTML

getTD-methods: Methods for function getTD

getText-methods: Methods for function getText

getURL-methods: Methods for function getURL

is.annpkg: Determine if packages contain annotation

selectorWidget: Dialog to select items from a list

Files in this package

annaffy/R/annotation.R annaffy/R/chkPkgs.R annaffy/R/search.R annaffy/R/table.R annaffy/R/widget.R annaffy/R/zzz.R
annaffy/man/aaf.character.Rd annaffy/man/aaf.goterm.Rd annaffy/man/aaf.handler.Rd annaffy/man/aaf.integer.Rd annaffy/man/aaf.raw.Rd annaffy/man/aafChromLoc-class.Rd annaffy/man/aafChromLoc.Rd annaffy/man/aafChromosome-class.Rd annaffy/man/aafChromosome.Rd annaffy/man/aafCytoband-class.Rd annaffy/man/aafCytoband.Rd annaffy/man/aafDescription-class.Rd annaffy/man/aafDescription.Rd annaffy/man/aafExpr.Rd annaffy/man/aafGO-class.Rd annaffy/man/aafGO.Rd annaffy/man/aafGOItem-class.Rd annaffy/man/aafGenBank-class.Rd annaffy/man/aafGenBank.Rd annaffy/man/aafIntensity-class.Rd annaffy/man/aafList-class.Rd annaffy/man/aafLocusLink-class.Rd annaffy/man/aafLocusLink.Rd annaffy/man/aafPathway-class.Rd annaffy/man/aafPathway.Rd annaffy/man/aafPathwayItem-class.Rd annaffy/man/aafProbe-class.Rd annaffy/man/aafProbe.Rd annaffy/man/aafPubMed-class.Rd annaffy/man/aafPubMed.Rd annaffy/man/aafSearchGO.Rd annaffy/man/aafSearchText.Rd annaffy/man/aafSigned-class.Rd annaffy/man/aafSymbol-class.Rd annaffy/man/aafSymbol.Rd annaffy/man/aafTable-class.Rd annaffy/man/aafTable.Rd annaffy/man/aafTableAnn.Rd annaffy/man/aafTableFrame.Rd annaffy/man/aafTableInt.Rd annaffy/man/aafUniGene-class.Rd annaffy/man/aafUniGene.Rd annaffy/man/chkPkgs.Rd annaffy/man/getCSS-methods.Rd annaffy/man/getHTML-methods.Rd annaffy/man/getTD-methods.Rd annaffy/man/getText-methods.Rd annaffy/man/getURL-methods.Rd annaffy/man/is.annpkg.Rd annaffy/man/selectorWidget.Rd

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