D_matrix: Calculate substitution rate matrix between two amino acids

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function is used to calculate Landgraf conservation metric. D_matrix contains substitution rates between two amino acids in the alignment, according to the following formula:

D(a,b)= (d(a,a)-d(a,b))/d(a,a)

where:
d(a,a) is a probability of AA substitution by itself
d(a,b) is a probability of substitution of amino acid a with other amino acid.

Usage

D_matrix(substitution_matrix)

Arguments

substitution_matrix

A matrix with probablity of substitutions, e.g. Gonnet substitution matrix

Value

A matrix of substitution probablities for all amino acids

Examples

data("gonnet")
distance=D_matrix(gonnet)

michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.