Calculate the covariance overlap obtained from NMA.
covsoverlap(...)# S3 method for enma
covsoverlap(enma, ncore=NULL, ...)
# S3 method for nma
covsoverlap(a, b, subset=NULL, ...)
Returns the similarity coefficient(s).
an object of class "enma" obtained from function
nma.pdbs.
number of CPU cores used to do the calculation.
ncore>1 requires package ‘parallel’ installed.
a list object with elements ‘U’ and ‘L’
(e.g. as obtained from function nma) containing the
eigenvectors and eigenvalues, respectively, to be
compared with b.
a list object with elements ‘U’ and ‘L’
(e.g. as obtained from function nma) containing the
eigenvectors and eigenvalues, respectively, to be
compared with a.
the number of modes to consider.
arguments passed to associated functions.
Lars Skjaerven
Covariance overlap is a measure for the similarity between two covariance matrices, e.g. obtained from NMA.
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Romo, T.D. et al. (2011) Proteins 79, 23--34.
Other similarity measures:
sip, covsoverlap, bhattacharyya.