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Lineal mutual information for ensemble NMA
Hi,
I would be interested in comparing the lineal mutual information coefficients for a set of structures, which are divided into two groups. I have already prepared an ensemble NMA, and there are clear dynamic differences in the fluctuations between the two groups. However, as far as I can see, only cross correlation is available for ensemble NMA. Is this correct, or did I miss something in the documentation?
Many thanks!
Comments (7)
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Hi,
You can use the
cov()
function to calculate the covariance and then use thecov2dccm()
function withmethod="lmi"
to get LMI. -
reporter Hi Xinqiu,
Thanks for your answer. I’ve tried to use the cov() function as shown in the documentation but it’s not working as it should.
> class(test) [1] "enma" # As shown in the docs for ensemble NMA > cov_matrix <- cov(test, ncore=NULL) Error in cov(test, ncore = NULL) : unused argument (ncore = NULL) # As shown for single structure NMA > cov_matrix <- cov(test) Error in cov(test) : supply both 'x' and 'y' or a matrix-like 'x'
Any ideas of what the problem could be? For reference, I am using bio3d v2.4-4.
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Can you try
cov.enma()
directly and see if it works? Also, if you want, you can attach an example “test” file for me to take a deeper look. -
reporter Hi Xinqiu,
Indeed, cov.enma() works. How do you go about using cov2dccm() since it’s not exported to the namespace? I’ve tried some variations around
bio3d:::dccm.xyz.cov2dccm(cov_matrix)
but I didn’t find what works. Apologies, I don’t use R regularly. This could be an addition to the docs.
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it should be
bio3d:::.cov2dccm()
, note that there is a period “.” before “cov”. -
reporter Brilliant, I got the linear mutual information matrix for each structure. Thanks a lot for your help!
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