Package ubic.erminej.data

Class Summary

Class	Description
AnnotationFileFetcher	Assistance in getting gene annotation files.
DataIOUtils
EmptyGeneSetResult	Placeholder for sets that were not used.
Gene	Represents a Gene entity.
GeneAnnotationParser	Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.
GeneAnnotations	Maintains gene annotations.
GeneScores	Parse and store probe->score associations.
GeneSet	A group of genes, such as those defined by GO annotations or KEGG pathways.
GeneSetDetails	Combination of scores and data for a gene set, for visualization
GeneSetDetailsImageWriter	Methods for writing a GeneSetDetails heatmap to a image file
GeneSetMapTools	Utility methods
GeneSetResult	Data structure to store class scoring information about a class.
GeneSetTerm	Represents a GO term (most commonly) or other way of grouping genes.
GeneSetTerms	Maintain information on GeneSetTerms (including but not limited GO terms).
GOParser	Read in the GO XML file provided by the Gene Ontology Consortium.
Histogram	Stores distributions for geneSets ( a series of histograms).
Multifunctionality	Implementation of multifunctionality computations as described in Gillis and Pavlidis (2011) PLoS ONE 6:2:e17258.
Probe	Represents an assayable item such as a microarray probe (or probeset) that can refer to more than one gene.
UserDefinedGeneSetManager	This is designed to work as a singleton in the scope of a running ErmineJ instance.

Enum Summary

Enum	Description
GeneAnnotationParser.Format
UserDefinedGeneSetManager.GeneSetFileFormat