R: Covariance Overlap

covsoverlap {bio3d}

R Documentation

Covariance Overlap

Description

Calculate the covariance overlap obtained from NMA.

Usage

covsoverlap(...)

## S3 method for class 'enma'
covsoverlap(enma, ncore=NULL, ...)

## S3 method for class 'nma'
covsoverlap(a, b, subset=NULL, ...)

Arguments

`enma`	an object of class `"enma"` obtained from function `nma.pdbs`.
`ncore`	number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.
`a`	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`.
`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`.
`subset`	the number of modes to consider.
`...`	arguments passed to associated functions.

Details

Covariance overlap is a measure for the similarity between two covariance matrices, e.g. obtained from NMA.

Value

Returns the similarity coefficient(s).

Author(s)

Lars Skjaerven

References

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.