hyperGtable {GOstats} | R Documentation

## (DEPRECATED) Table from GOHyperG

### Description

Use the `summary` method on a `GOHyperGResult` object.

Output a table from a call to `GOHyperG`.

### Usage

    hyperGtable(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
    save = FALSE, output = TRUE, filename = NULL, universe = NULL)

### Arguments

`probids` | A vector of Affymetrix probe IDs
`lib` | An annotation package (e.g., `hgu95av2`)
`type` | One of "MF", "CC", "BP", indicating molecular function, cellular component, or biological process, respectively.
`pvalue` | The significance level used to choose GO terms
`min.count` | The minimum number of a given GO term that must be on the chip in order to choose that GO term. This protects against very low p-values that result from the situation where there are very few genes with a given GO term on the chip, but one or two are found in the set of significant genes.
`save` | Boolean - Set to `TRUE` to save the resulting `data.frame`.
`output` | Boolean - Set to `TRUE` to output the resulting `data.frame` as a text file.
`filename` | If output is set to `TRUE`, give the file name for the output file.
`universe` | A character vector of unique Entrez Gene identifiers or `NULL`. This is the population (the urn) of the Hypergeometric test. When `NULL` (default), the population is all Entrez Gene ids in the annotation package that have a GO term annotation in the specified GO category (see `GOHyperG` for more details).

### Details

This function will take a vector of Affymetrix IDs and output a `data.frame` containing information on all GO terms that are found significant in a call to `GOHyperG`.

### Value

A `data.frame` containing the following columns:
GO Term - The GOID associated with a given GO term
Description - The description for that GO term
p-values - The p-value associated with that GO term
Number significant - The number of genes in the vector of Affymetrix IDs with that particular GO term
Number on chip - The number of genes on the Affymetrix chip with that particular GO term.

### Author(s)

James W. MacDonald <jmacdon@med.umich.edu>

### Examples

    ## Not run:
    library("hgu95av2")
    probids <- ls(hgu95av2GENENAME)[1:10]
    hyperGtable(probids, "hgu95av2", save = TRUE, output = FALSE)
    ## End(Not run)

[Package GOstats version 2.2.6 Index]