hyperG2Affy {GOstats} | R Documentation

## A List of Affymetrix IDs from GOIDs

### Description

Output a list of Affymetrix IDs associated with each significant GOID, based on the output from hyperGtable.

### Usage

    hyperG2Affy(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
    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.
`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

The function `hyperGtable` will output a table listing a set of GOIDs that are significantly over-represented in a set of significant genes. The next logical step might be to look at the individual genes that are represented by each GOID. This function will output the Affymetrix IDs for each GOID in a list, which can then be used to either output HTML tables using `probes2table`, or possibly just output the gene names for each GOID.

### Value

A named `list` with all the Affymetrix IDs associated with each significant GOID.

### Author(s)

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

### Examples

    library("hgu95av2")
    probids <- ls(hgu95av2GENENAME)[1:10]
    hyperG2Affy(probids, "hgu95av2")

[Package GOstats version 2.0.4 Index]