D_matrix {BALCONY} | R Documentation |
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.
D_matrix(substitution_matrix)
substitution_matrix |
A matrix with probablity of substitutions, e.g. Gonnet substitution matrix |
distance |
A matrix of substitution probablities for all amino acids |
Alicja Pluciennik & Michal Stolarczyk
data("gonnet") distance=D_matrix(gonnet)