OBOHyperGResult-class: Class "OBOHyperGResult"
In GOstats: Tools for manipulating GO and microarrays

Description Objects from the Class Slots Extends Methods Author(s) See Also

This class represents the results of a test for overrepresentation of OBO categories among genes in a selected gene set based upon the Hypergeometric distribution.

For details on extracting information from this object, be sure to read the accessor documentation in the Category package: HyperGResult-accessors.

Objects can be created by calls of the form new("OBOHyperGResult", ...).

goDag:: Object of class "graph" representing the DAG of OBO terms tested.
pvalue.order:: Object of class "integer". The sort order of the computed p-values.
annotation:: Object of class "character". The name of the annotation data package used in the analysis.
geneIds:: Object of class "ANY". The intersection of the gene identifiers given as input and the computed gene universe.
testName:: Object of class "character". Identifies the testing method used to produce this result instance.
pvalueCutoff:: Object of class "numeric". The cutoff for significance used for some testing methods. Also used for pretty display in the show method.
conditional:: A logical indicating whether the calculation should condition on the OBO structure.
testDirection:: A string which can be either "over" or "under". This determines whether the test performed detects over or under represented OBO terms.

Class "HyperGResultBase", directly.

goDag: signature(r = "OBOHyperGResult"): return the graph instance representing the DAG of the OBO terms that were tested.
summary: signature(r = "OBOHyperGResult"): Returns a data.frame summarizing the test result. Optional arguments pvalue and categorySize allow specification of maximum p-value and minimum categorySize, respectively. Optional argument htmlLinks is a logical value indicating whether to add HTML links (useful in conjunction with xtables print method with type set to "html").
htmlReport: signature(r = "OBOHyperGResult"): Write an HTML version of the table produced by the summary method. The path of a file to write the report to can be specified using the file argument. The default is file="" which will cause the report to be printed to the screen. If you wish to create a single report comprising multiple results you can set append=TRUE. The default is FALSE (overwrite preexisting report file). You can specify a string to use as an identifier for each table by providing a value for the label argument. Additional named arguments will be passed to the summary method.
description: signature(object = "OBOHyperGResult"): Return a string giving a one-line description of the result.