GOHyperGResult-class {GOstats} | R Documentation

## 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.

### 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.

### Extends

Class `"HyperGResultBase"`, directly.

### Methods

geneCounts
  `signature(r = "GOHyperGResult")`: return an `"integer"` vector: for each category term tested, the number of genes from the gene set that are annotated at the term.
goDag
  `signature(r = "GOHyperGResult")`: return the `graph` instance representing the DAG of the GO terms that were tested.
pvalues
  `signature(r = "GOHyperGResult")`: return a `"numeric"` vector: the ordered p-values for each category term tested.
oddsRatios
  `signature(r = "GOHyperGResult")`: return a `"numeric"` vector: the odds ratio for each category term tested.
expectedCounts
  `signature(r = "GOHyperGResult")`: return a `"numeric"` vector: the expected number of genes for each GO term tested.
universeCounts
  `signature(r = "GOHyperGResult")`: return an `"integer"` vector: for each category term tested, the number of genes from the gene universe that are annotated at the term.
universeMappedCount
  `signature(r = "GOHyperGResult")`: return an `"integer"` vector of length one giving the size of the gene universe set.
geneIdUniverse
  `signature(r = "GOHyperGResult")`: return a list named by the tested GO terms. Each element of the list is a vector of gene identifiers (from the gene universe) annotated at the corresponding GO term.
condGeneIdUniverse
  `signature(r = "GOHyperGResult")`: return a list named by the tested GO terms. Each element of the list is a vector of the remaining gene identifiers (from the gene universe) annotated at the corresponding GO term after the identifiers from significant children were removed. This is only available when the calculation performed used the conditional Hypergeometric algorithm.
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 cateogyrSize, 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.
isConditional
  `signature(r = "GOHyperGResult")`: Return a `TRUE` if the result was created using a conditional algorithm and `FALSE` otherwise.

### Author(s)

Seth Falcon

### See Also

`GeneCategoryHyperGeoTestResult`

[Package GOstats version 2.0.4 Index]