GOstats-defunct {GOstats}R Documentation

Defunct Functions in GOstats Package

Description

The functions or variables listed here are no longer part of GOstats as they are not needed (any more).

Usage

combGOGraph(g1, g2)
hyperGtable(probids, lib, type="MF", pvalue=0.05,
                        min.count=10, save = FALSE, output = TRUE,
                        filename = NULL, universe = NULL)
hyperG2Affy(probids, lib, type="MF", pvalue=0.05,
                         min.count=10, universe = NULL)

Arguments

g1 A graph
g2 A graph
probids A vector of Affymetrix probe IDs
lib An annotation package (e.g., hgu95av2.db)
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).
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.

Details

combGOGraph was replaced by join. hyperGtable was replaced by summary. hyperG2Affy was replaced by probeSetSummary.


[Package GOstats version 2.4.0 Index]