fisherExactTest: Measure over-representation using Fisher's Exact Test

In martingarridorc/biokit: Toolkit for the automatic analysis of omics data

Description

Uses fisher.test to calculate the over-representation of a set of features on a functional category given an "universe" that is used as statistical background. Based on the Fisher's Exact Test over a contingency table.

Usage

fisherExactTest(features, funCat, universe)

Arguments

features	Input features.
funCat	All the features in the functional category.
universe	All the universe features.

Value

The over-representation significance as a P value.

Examples

g <- letters[1:5]
f <- letters[2:6]
f2 <- letters[c(1, 10:15)]
u <- letters

# this should give a low p value (high over-representation)
fisherExactTest(g, f, u)
# this should give a high p value (low over-representation)
fisherExactTest(g, f2, u)

martingarridorc/biokit documentation built on June 28, 2021, 12:24 a.m.