annaffy: Annotation tools for Affymetrix biological metadata

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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.

Author
Colin A. Smith <colin@colinsmith.org>
Date of publication
None
Maintainer
Colin A. Smith <colin@colinsmith.org>
License
LGPL
Version
1.46.0

View on Bioconductor

Man pages

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/COPYING
annaffy/DESCRIPTION
annaffy/NAMESPACE
annaffy/R
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/build
annaffy/build/vignette.rds
annaffy/data
annaffy/data/aafExpr.rda
annaffy/inst
annaffy/inst/doc
annaffy/inst/doc/annaffy.R
annaffy/inst/doc/annaffy.Rnw
annaffy/inst/doc/annaffy.pdf
annaffy/man
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
annaffy/vignettes
annaffy/vignettes/annaffy.Rnw
annaffy/vignettes/selector.png