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annaffy (version 1.40.0)

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

1.40.0

License

LGPL

Maintainer

Colin A Smith

Last Published

February 15th, 2017

Functions in annaffy (1.40.0)

aafChromosome

Constructor for aafChromosome objects
aafCytoband-class

Class aafCytoband, a class for cytoband data
.aaf.goterm

Fetch Gene Ontology term information
.aaf.character

Generic constructor for classes extending character
.aaf.integer

Generic constructor for classes extending integer
.aaf.raw

Fetch raw annotation data
aafChromLoc-class

Class aafChromLoc, a class for gene chromosome locations
aaf.handler

Handle feching annotation data columns
aafChromLoc

Constructor for aafChromLoc objects
aafChromosome-class

Class aafChromosome, a class for gene chromosome assignments
aafGO

Constructor for aafGO objects
aafDescription-class

Class aafDescription, a class for gene descriptions
aafIntensity-class

Class aafIntensity, a class for gene expression values
aafDescription

Constructor for aafDescription objects
aafGenBank

Constructor for aafGenBank objects
aafExpr

Sample ExpressionSet used for demonstration purposes
aafGenBank-class

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

Class aafGO, a class for gene ontology ids
aafCytoband

Constructor for aafCytoband objects
aafGOItem-class

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

Class aafLocusLink, a class for LocusLink ids
aafList-class

Class aafList, a specialized subclass of list
aafPathway-class

Class aafPathway, a class for KEGG pathway ids
aafPathway

Constructor for aafPathway objects
aafPubMed

Constructor for aafPubMed objects
aafPubMed-class

Class aafPubMed, a class for PubMed 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
aafLocusLink

Constructor for aafLocusLink objects
aafSigned-class

Class aafSigned, a class for signed numerical data
aafTableFrame

Constructor for aafTable objects from data frames
aafTable

Constructor for aafTable objects
aafSymbol

Constructor for aafSymbol objects
aafTableInt

Constructor for aafTable objects from ExpressionSets
aafSymbol-class

Class aafSymbol, a class for gene symbols
aafSearchGO

Find probe ids corresponding to GO ids
aafTable-class

Class aafTable, a tabular microarray data class
aafSearchText

Search metadata annotation text
aafTableAnn

Constructor for aafTable objects from annotation data
getHTML-methods

Methods for function getHTML
getText-methods

Methods for function getText
aafUniGene

Constructor for aafUniGene objects
selectorWidget

Dialog to select items from a list
getTD-methods

Methods for function getTD
getCSS-methods

Methods for function getCSS
chkPkgs

A Function to Check for and Install Missing Annotation Packages
aafUniGene-class

Class aafUniGene, a class for UniGene cluster ids
getURL-methods

Methods for function getURL
is.annpkg

Determine if packages contain annotation