Annotation tools for Affymetrix biological metadata

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Documentation for package ‘annaffy’ version 1.42.0

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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
aafUniGene Constructor for aafUniGene objects
aafUniGene-class Class aafUniGene, a class for UniGene cluster ids

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