topGO (version 2.24.0)

Gene set tests statistics: Gene set tests statistics

Description

Methods which implement and run a group test statistic for a class inheriting from groupStats class. See Details section for a description of each method.

Usage

GOFisherTest(object)
GOKSTest(object)
GOtTest(object)
GOglobalTest(object)
GOSumTest(object)
GOKSTiesTest(object)

Arguments

object

An object of class groupStats or decedent class.

Value

All these methods return the p-value computed by the respective test statistic.

Details

GOFisherTest: implements Fischer's exact test (based on contingency table) for groupStats objects dealing with "counts". GOKSTest: implements the Kolmogorov-Smirnov test for groupStats objects dealing with gene "scores". This test uses the ks.test function and does not implement the running-sum-statistic test based on permutations.

GOtTest: implements the t-test for groupStats objects dealing with gene "scores". It should be used when the gene scores are t-statistics or any other score following a normal distribution. GOglobalTest: implement Goeman's globaltest.

See Also

groupStats-class, getSigGroups-methods