OBOHyperGResult-class {GOstats} | R Documentation

## Class "OBOHyperGResult"

### Description

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 from the Class

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

### Slots

`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.

### Extends

Class `"HyperGResultBase"`, directly.

### Methods

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.

### Author(s)

Robert Castelo

### See Also

HyperGResult-accessors

[Package GOstats version 2.53.0 Index]