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annaffy (version 1.38.0)

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

1.38.0

License

LGPL

Maintainer

Colin A Smith

Last Published

February 15th, 2017

Functions in annaffy (1.38.0)

Fetch Gene Ontology term information

Constructor for aafChromLoc objects

aafChromosome-class

Class aafChromosome, a class for gene chromosome assignments

Fetch raw annotation data

aafCytoband-class

Class aafCytoband, a class for cytoband data

Constructor for aafChromosome objects

Handle feching annotation data columns

Generic constructor for classes extending integer

aafChromLoc-class

Class aafChromLoc, a class for gene chromosome locations

Generic constructor for classes extending character

aafGenBank-class

Class aafGenBank, a class for GenBank accession numbers

Constructor for aafCytoband objects

Class aafGO, a class for gene ontology ids

Constructor for aafDescription objects

aafGOItem-class

Class aafGOItem, a class for gene ontology id elements

Constructor for aafGenBank objects

aafIntensity-class

Class aafIntensity, a class for gene expression values

Sample ExpressionSet used for demonstration purposes

Constructor for aafGO objects

Class aafProbe, a class for Probe ids

Constructor for aafProbe objects

Class aafList, a specialized subclass of list

aafDescription-class

Class aafDescription, a class for gene descriptions

aafPathway-class

Class aafPathway, a class for KEGG pathway ids

Constructor for aafLocusLink objects

aafLocusLink-class

Class aafLocusLink, a class for LocusLink ids

Constructor for aafPathway objects

aafPathwayItem-class

Class aafPathwayItem, a class for KEGG pathway id elements

aafPubMed-class

Class aafPubMed, a class for PubMed ids

Constructor for aafPubMed objects

aafSymbol-class

Class aafSymbol, a class for gene symbols

aafSigned-class

Class aafSigned, a class for signed numerical data

Class aafTable, a tabular microarray data class

Constructor for aafSymbol objects

Constructor for aafTable objects from annotation data

getText-methods

Methods for function getText

Constructor for aafTable objects

Methods for function getURL

A Function to Check for and Install Missing Annotation Packages

Methods for function getCSS

Constructor for aafTable objects from data frames

Dialog to select items from a list

Constructor for aafTable objects from ExpressionSets

Find probe ids corresponding to GO ids

Determine if packages contain annotation

Search metadata annotation text

getHTML-methods

Methods for function getHTML

aafUniGene-class

Class aafUniGene, a class for UniGene cluster ids

Methods for function getTD

Constructor for aafUniGene objects