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]