hyperG2Affy {GOstats}R Documentation

(DEPRECATED) A List of Affymetrix IDs from GOIDs

Description

Use probeSetSummary instead.

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

## Not run: 
library("hgu95av2")
probids <- ls(hgu95av2GENENAME)[1:10]
hyperG2Affy(probids, "hgu95av2")
## End(Not run)

[Package GOstats version 2.2.6 Index]