jaccard.rahman: Compute p-value using an extreme value distribution

In jaccard: Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients

Description

Rahman et al. (2014) proposes a method to compute a p-value of a Jaccard/Tanimoto coefficient using an extreme value distribution. Their paper provides the following description: The mean (mu) and s.d. (sigma) of the similarity scores are used to define the z score, z = (Tw - mu)/sigma. For the purpose of calculating the P value, only hits with T > 0 are considered. The P value w is derived from the z score using an extreme value distribution P = 1 - exp(-e-z*pi/sqrt(6) - G'(1)), where the Euler=Mascheroni constant G'(1)=0.577215665.

Usage

jaccard.rahman(j)

Arguments

j	a numeric vector of observed Jaccard coefficients (uncentered)

Value

jaccard.rahman returns a numeric vector of p-values

References

Rahman, Cuesta, Furnham, Holliday, and Thornton (2014) EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature Methods, 11(2) http://www.nature.com/nmeth/journal/v11/n2/full/nmeth.2803.html

jaccard documentation built on May 2, 2019, 12:51 p.m.