HyperGResultBase-class {Category}R Documentation

Class "HyperGResultBase"

Description

This VIRTUAL class represents common elements of the return values of generic functions like hyperGTest.

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

annotation:
Object of class "character" giving the name of the annotation data package used.
geneIds:
Object of class "ANY" (usually a character vector, but sometimes an integer vector). The input vector of gene identifiers intersected with the universe of gene identifiers used in the computation.
testName:
Object of class "character" identifying the testing method used.
pvalueCutoff:
Numeric value used by the testing method as a p-value cutoff. Not all testing methods use this. Also used by the show method to count number of significant terms.
testDirection:
A string indicating whether the test performed was for overrepresentation ("over") or underrepresentation("under").

Methods

annotation
signature(object = "HyperGResultBase"): return the name of the annotation data package used.
geneIds
signature(r = "HyperGResultBase"): return the input vector of gene identifiers intersected with the universe of gene identifiers used in the computation.
geneMappedCount
signature(r = "HyperGResultBase"): return the size of the selected gene set used in the computation. This is simply the length(geneIds(obj)).
pvalueCutoff
signature(r = "HyperGResultBase"): accessor for the pvalueCutoff slot.
testDirection
signature(r = "HyperGResultBase"): accessor for the testDirection slot. Contains a string indicating whether the test was for "over" or "under" representation of the categories.
description
signature(object = "HyperGResultBase"): return a character string description of the test result.
show
signature(object = "HyperGResultBase"): display an instance.
testName
signature(r = "HyperGResultBase"): return a string describing the testing method used.
isConditional(r)
Return TRUE if the result was obtained using a conditional algorithm.
summary
signature(r = "HyperGResultBase"): Returns a data.frame summarizing the test result. Optional arguments pvalue and categorySize allow specification of maximum p-value and minimum cateogyrSize, respectively.
htmlReport
signature(r = "HyperGResultBase"): 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.

Author(s)

Seth Falcon

See Also

HyperGResult-class GeneGoHyperGeoTestResult-class


[Package Category version 2.0.3 Index]