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 <colin@colinsmith.org>
Date of publicationNone
MaintainerColin A. Smith <colin@colinsmith.org>
LicenseLGPL
Version1.46.0

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

Functions

.aaf.character Man page
aafChromLoc Man page
aafChromLoc-class Man page
aafChromosome Man page
aafChromosome-class Man page
aafCytoband Man page
aafCytoband-class Man page
aafDescription Man page
aafDescription-class Man page
aafExpr Man page
aafGenBank Man page
aafGenBank-class Man page
aafGO Man page
aafGO-class Man page
aafGOItem Man page
aafGOItem-class Man page
.aaf.goterm Man page
aaf.handler Man page
.aaf.integer Man page
aafIntensity Man page
aafIntensity-class Man page
aafList Man page
aafList-class Man page
[,aafList-method Man page
aafLocusLink Man page
aafLocusLink-class Man page
aafPathway Man page
aafPathway-class Man page
aafPathwayItem Man page
aafPathwayItem-class Man page
aafProbe Man page
aafProbe-class Man page
aafPubMed Man page
aafPubMed-class Man page
.aaf.raw Man page
aafSearchGO Man page
aafSearchText Man page
aafSigned Man page
aafSigned-class Man page
aafSymbol Man page
aafSymbol-class Man page
aafTable Man page
$.aafTable Man page
aafTableAnn Man page
aafTable-class Man page
aafTableFrame Man page
aafTableInt Man page
[,aafTable-method Man page
[[,aafTable-method Man page
aafUniGene Man page
aafUniGene-class Man page
chkPkgs Man page
colnames Man page
colnames<- Man page
colnames<-,aafTable-method Man page
colnames,aafTable-method Man page
dim.aafTable Man page
getCSS Man page
getCSS,aafGO-method Man page
getCSS,aafList-method Man page
getCSS,aafPathway-method Man page
getCSS,aafPubMed-method Man page
getCSS,aafSigned-method Man page
getCSS,ANY-method Man page
getCSS-methods Man page
getHTML Man page
getHTML,aafGOItem-method Man page
getHTML,aafGO-method Man page
getHTML,aafList-method Man page
getHTML,aafPathwayItem-method Man page
getHTML,aafPathway-method Man page
getHTML,aafPubMed-method Man page
getHTML,aafUniGene-method Man page
getHTML,ANY-method Man page
getHTML-methods Man page
getTD Man page
getTD,aafGO-method Man page
getTD,aafIntensity-method Man page
getTD,aafList-method Man page
getTD,aafPathway-method Man page
getTD,aafPubMed-method Man page
getTD,aafSigned-method Man page
getTD,ANY-method Man page
getTD-methods Man page
getText Man page
getText,aafCytoband-method Man page
getText,aafGOItem-method Man page
getText,aafGO-method Man page
getText,aafList-method Man page
getText,aafPathwayItem-method Man page
getText,aafPathway-method Man page
getText,ANY-method Man page
getText-methods Man page
getURL Man page
getURL,aafCytoband-method Man page
getURL,aafGenBank-method Man page
getURL,aafGOItem-method Man page
getURL,aafGO-method Man page
getURL,aafList-method Man page
getURL,aafLocusLink-method Man page
getURL,aafPathwayItem-method Man page
getURL,aafPathway-method Man page
getURL,aafProbe-method Man page
getURL,aafPubMed-method Man page
getURL,aafUniGene-method Man page
getURL,ANY-method Man page
getURL-methods Man page
is.annpkg Man page
merge.aafTable Man page
probeids Man page
probeids<- Man page
probeids<-,aafTable-method Man page
probeids,aafTable-method Man page
rbind.aafTable Man page
saveHTML Man page
saveHTML,aafTable-method Man page
saveText Man page
saveText,aafTable-method Man page
selectorWidget Man page
show,aafCytoband-method Man page
show,aafGOItem-method Man page
show,aafList-method Man page
show,aafPathwayItem-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.