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, ...)
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.
Returns the similarity coefficient(s).
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
.