Measure over-representation using Fisher's Exact Test

Source: R/over_representation_analysis.R

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.

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)

#> [1] 0.001611432
# this should give a high p value (low over-representation)
fisherExactTest(g, f2, u)

#> [1] 0.8232289