Category-defunct
(Package: Category) :
Defunct Functions in Package pkg{Category
The functions or variables listed here are no longer part of the Category package.
● Data Source:
BioConductor
● Keywords:
● Alias: Category-defunct
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This class represents chromosome band annotation data for a given experiment. The class is responsible for storing the mapping of band to set of gene IDs located within that band as well as for representing the tree structured relationship among the bands.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ChrBandTree-class
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This class encapsulates parameters needed for Hypergeometric testing of over or under representation of chromosome bands among a selected gene list using hyperGTest.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ChrMapHyperGParams-class
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This class represents the results of a Hypergeometric test for over-representation of genes in a selected gene list in the chromosome band annotation. The hyperGTest function returns an instance of ChrMapHyperGResult when given a parameter object of class ChrMapHyperGParams. For details on accessing the results, see HyperGResult-accessors.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ChrMapHyperGResult-class
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This class encapsulates parameters needed for testing systematic variations in some gene-level statistic by chromosome bands using linearMTest.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ChrMapLinearMParams-class
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This class represents the results of a linear model-based test for systematic changes in a per-gene statistic by chromosome band annotation. The linearMTest function returns an instance of ChrMapLinearMResult when given a parameter object of class ChrMapLinearMParams. Most slots can be queried using accessors.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ChrMapLinearMResult-class
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DatPkg is a VIRTUAL class for representing annotation data packages.
● Data Source:
BioConductor
● Keywords: classes
● Alias: AffyDatPkg-class, DatPkg-class, GeneSetCollectionDatPkg, Org.XX.egDatPkg-class, YeastDatPkg-class
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A parameter class for representing all parameters needed for running the hyperGTest method with one of the GO ontologies (BP, CC, MF) as the category.
● Data Source:
BioConductor
● Keywords: classes
● Alias: GOHyperGParams-class, categoryName,GOHyperGParams-method, show,GOHyperGParams-method
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GSEAGOHyperGParams
(Package: Category) :
Helper function for constructing a GOHyperGParams objects or
Helps to create A parameter class for representing all parameters needed for running the hyperGTest method. If it is a GOHyperGParams object, being made, then with one of the GO ontologies (BP, CC, MF) as the category. This function will construct the parameter object from a GeneSetCollection object and if necessary will also try to check to make sure that the object is based on a GO2ALL mapping.
● Data Source:
BioConductor
● Keywords: classes
● Alias: GSEAGOHyperGParams, GSEAKEGGHyperGParams
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An abstract (VIRTUAL) parameter class for representing all parameters needed by a method specializing the hyperGTest generic. You should only use subclasses of this class directly.
● Data Source:
BioConductor
● Keywords: classes
● Alias: conditional, conditional<-, geneIds<-, ontology, ontology<-, pvalueCutoff<-, testDirection<-, universeGeneIds
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