jaccard.rahman: Compute p-value using the EC-BLAST method

In ncchung/jaccard: Testing similarity between binary datasets using Jaccard/Tanimoto coefficients

Description

In the EC-BLAST paper, Rahman et al. (2014) provide the following description: The mean (μ) and s.d. (σ) of the similarity scores are used to define the z score, z = (Tw – μ)/σ. 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−zπ/√(6) − Γ′ (1)), where the Euler-Mascheroni constant Γ′ (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

ncchung/jaccard documentation built on Dec. 31, 2019, 8:20 p.m.