GOHyperGResult-class: Class "GOHyperGResult"

In Bioconductor/GOstats: Tools for manipulating GO and microarrays

Class "GOHyperGResult"

Description

This class represents the results of a test for overrepresentation of GO 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 from the Class

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

Slots

goDag:

Object of class "graph" representing the DAG of GO 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 GO structure.

testDirection:

A string which can be either "over" or "under". This determines whether the test performed detects over or under represented GO terms.

Extends

Class "HyperGResultBase", directly.

Methods

goDag

signature(r = "GOHyperGResult"): return the graph instance representing the DAG of the GO terms that were tested.

summary

signature(r = "GOHyperGResult"): 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 = "GOHyperGResult"): 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 = "GOHyperGResult"): Return a string giving a one-line description of the result.

Author(s)

Seth Falcon

See Also

HyperGResult-accessors

Bioconductor/GOstats documentation built on Nov. 2, 2024, 6:34 a.m.