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annaffy (version 1.44.0)

Annotation tools for Affymetrix biological metadata

Description

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.

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Version

Version

1.44.0

License

LGPL

Maintainer

Colin A Smith

Last Published

February 15th, 2017

Functions in annaffy (1.44.0)

aafTable-class

Class aafTable, a tabular microarray data class
getHTML-methods

Methods for function getHTML
aafSigned-class

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

Class aafIntensity, a class for gene expression values
aafSearchText

Search metadata annotation text
aafList-class

Class aafList, a specialized subclass of list
aafExpr

Sample ExpressionSet used for demonstration purposes
aafGOItem-class

Class aafGOItem, a class for gene ontology id elements
aafLocusLink

Constructor for aafLocusLink objects
aafGO

Constructor for aafGO objects
aafChromLoc-class

Class aafChromLoc, a class for gene chromosome locations
aafTableFrame

Constructor for aafTable objects from data frames
aafSymbol

Constructor for aafSymbol objects
.aaf.integer

Generic constructor for classes extending integer
.aaf.raw

Fetch raw annotation data
getTD-methods

Methods for function getTD
aafUniGene-class

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

Class aafDescription, a class for gene descriptions
aafSearchGO

Find probe ids corresponding to GO ids
aafPubMed

Constructor for aafPubMed objects
aafPathwayItem-class

Class aafPathwayItem, a class for KEGG pathway id elements
getCSS-methods

Methods for function getCSS
aafChromosome-class

Class aafChromosome, a class for gene chromosome assignments
aafChromLoc

Constructor for aafChromLoc objects
aafGenBank

Constructor for aafGenBank objects
aafChromosome

Constructor for aafChromosome objects
aafTable

Constructor for aafTable objects
selectorWidget

Dialog to select items from a list
aafSymbol-class

Class aafSymbol, a class for gene symbols
aafCytoband

Constructor for aafCytoband objects
aaf.handler

Handle feching annotation data columns
.aaf.goterm

Fetch Gene Ontology term information
aafDescription

Constructor for aafDescription objects
aafPubMed-class

Class aafPubMed, a class for PubMed ids
aafTableInt

Constructor for aafTable objects from ExpressionSets
aafTableAnn

Constructor for aafTable objects from annotation data
aafUniGene

Constructor for aafUniGene objects
getURL-methods

Methods for function getURL
aafProbe

Constructor for aafProbe objects
getText-methods

Methods for function getText
aafPathway-class

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

Class aafLocusLink, a class for LocusLink ids
chkPkgs

A Function to Check for and Install Missing Annotation Packages
is.annpkg

Determine if packages contain annotation
aafProbe-class

Class aafProbe, a class for Probe ids
.aaf.character

Generic constructor for classes extending character
aafGO-class

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

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

Class aafCytoband, a class for cytoband data
aafPathway

Constructor for aafPathway objects