Annotation tools for Affymetrix biological metadata

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Documentation for package ‘annaffy’ version 1.72.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

A C D G I M P R S misc

-- A --

aaf.handler	Handle feching annotation data columns
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 aafGOItem, a class for gene ontology id elements
aafGOItem-class	Class aafGOItem, a class for gene ontology id elements
aafIntensity	Class aafIntensity, a class for gene expression values
aafIntensity-class	Class aafIntensity, a class for gene expression values
aafList	Class aafList, a specialized subclass of list
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 aafPathwayItem, a class for KEGG pathway id elements
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
aafSearchGO	Find probe ids corresponding to GO ids
aafSearchText	Search metadata annotation text
aafSigned	Class aafSigned, a class for signed numerical data
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
aafTable-class	Class aafTable, a tabular microarray data class
aafTableAnn	Constructor for aafTable objects from annotation data
aafTableFrame	Constructor for aafTable objects from data frames
aafTableInt	Constructor for aafTable objects from ExpressionSets

-- C --

colnames	Class aafTable, a tabular microarray data class
colnames-method	Class aafTable, a tabular microarray data class
colnames<-	Class aafTable, a tabular microarray data class
colnames<--method	Class aafTable, a tabular microarray data class

-- D --

dim.aafTable

Class aafTable, a tabular microarray data class

-- G --

getCSS	Methods for function getCSS
getCSS-method	Class aafGO, a class for gene ontology ids
getCSS-method	Class aafList, a specialized subclass of list
getCSS-method	Class aafPathway, a class for KEGG pathway ids
getCSS-method	Class aafPubMed, a class for PubMed ids
getCSS-method	Class aafSigned, a class for signed numerical data
getCSS-method	Methods for function getCSS
getCSS-methods	Methods for function getCSS
getHTML	Methods for function getHTML
getHTML-method	Class aafGO, a class for gene ontology ids
getHTML-method	Class aafGOItem, a class for gene ontology id elements
getHTML-method	Class aafList, a specialized subclass of list
getHTML-method	Class aafPathway, a class for KEGG pathway ids
getHTML-method	Class aafPathwayItem, a class for KEGG pathway id elements
getHTML-method	Class aafPubMed, a class for PubMed ids
getHTML-method	Methods for function getHTML
getHTML-methods	Methods for function getHTML
getTD	Methods for function getTD
getTD-method	Class aafGO, a class for gene ontology ids
getTD-method	Class aafIntensity, a class for gene expression values
getTD-method	Class aafList, a specialized subclass of list
getTD-method	Class aafPathway, a class for KEGG pathway ids
getTD-method	Class aafPubMed, a class for PubMed ids
getTD-method	Class aafSigned, a class for signed numerical data
getTD-method	Methods for function getTD
getTD-methods	Methods for function getTD
getText	Methods for function getText
getText-method	Class aafCytoband, a class for cytoband data
getText-method	Class aafGO, a class for gene ontology ids
getText-method	Class aafGOItem, a class for gene ontology id elements
getText-method	Class aafList, a specialized subclass of list
getText-method	Class aafPathway, a class for KEGG pathway ids
getText-method	Class aafPathwayItem, a class for KEGG pathway id elements
getText-method	Methods for function getText
getText-methods	Methods for function getText
getURL	Methods for function getURL
getURL-method	Class aafCytoband, a class for cytoband data
getURL-method	Class aafGO, a class for gene ontology ids
getURL-method	Class aafGOItem, a class for gene ontology id elements
getURL-method	Class aafGenBank, a class for GenBank accession numbers
getURL-method	Class aafList, a specialized subclass of list
getURL-method	Class aafLocusLink, a class for LocusLink ids
getURL-method	Class aafPathway, a class for KEGG pathway ids
getURL-method	Class aafPathwayItem, a class for KEGG pathway id elements
getURL-method	Class aafProbe, a class for Probe ids
getURL-method	Class aafPubMed, a class for PubMed ids
getURL-method	Methods for function getURL
getURL-methods	Methods for function getURL

-- I --

is.annpkg

Determine if packages contain annotation

-- M --

merge.aafTable

Class aafTable, a tabular microarray data class

-- P --

probeids	Class aafTable, a tabular microarray data class
probeids-method	Class aafTable, a tabular microarray data class
probeids<-	Class aafTable, a tabular microarray data class
probeids<--method	Class aafTable, a tabular microarray data class

-- R --

rbind.aafTable

Class aafTable, a tabular microarray data class

-- S --

saveHTML	Class aafTable, a tabular microarray data class
saveHTML-method	Class aafTable, a tabular microarray data class
saveText	Class aafTable, a tabular microarray data class
saveText-method	Class aafTable, a tabular microarray data class
selectorWidget	Dialog to select items from a list
show-method	Class aafCytoband, a class for cytoband data
show-method	Class aafGOItem, a class for gene ontology id elements
show-method	Class aafList, a specialized subclass of list
show-method	Class aafPathwayItem, a class for KEGG pathway id elements

-- misc --

$.aafTable	Class aafTable, a tabular microarray data class
[-method	Class aafList, a specialized subclass of list
[-method	Class aafTable, a tabular microarray data class
[[-method	Class aafTable, a tabular microarray data class