could not interpret terms "node centrality", "betweenness centrality" "suboptimal paths"
Hello sir,
can you please simplify these above terms and also can you let us know how to implement these in network analysis.
Also in the tutorial, "cna_vintage.pdf(protein structure network with bio3d)" , page# 20 , figure:19, i have confusions on path length distributions as follows: 1. 1st figure shows the probability density axis starts from 0 to 120. Is that obvious?(i mean max. proabity can be 1, forgive me if i am wrong) 2.the path length in x axis is in angstrom(i hope).
- you have defined node degeneracy as number of paths passing through each node;
now in the Node degeneracy figure, it seems that node
#32has 50 number of path, so for me the node degeneracy of node#32is 50 instead of 1(as the node degeneracy table shows). table also shows for node#46, the degeneracy is 0.12, what does that mean?
looking forward your response, kajwal
Comments (5)
-
-
Hi,
All these terms and how they can be implemented with bio3d have been documented in the "cna_vignette.pdf". Please read the tutorial carefully and post more specific questions if you are still unclear after reading.
-
It is probability density not probability. Probability density can be larger than 1 but the integration over x-axis is 1.
-
Path length here indicates the coupling strength between two distal sites and does NOT represent the length of a "physical" path. Mathematically, path length is the sum of
-log(cij)
, where cij is the correlation value between two residues along the path. Therefore, it does not have a unit. -
The node degeneracy shown in the table is normalized. You can print non-normalized with
print(pa, normalize=FALSE)
and then you get the same results as shown in the figure.
-
-
reporter Dear sir,
in sub optimal path calculations,
pa <- cnapath(net, from=32, to=131, k=50
when k=50, we explore 50 suboptimal paths. But when i dont specify the k value, it explores 10 paths, so (i) Is 10 the default vaue of k? and (ii)how can i know the exact no of paths between the source and the sink?..
-
Yes, the default value of k is 10. There is no functionality to estimate the "exact" number of paths but usually we set 500 and it will give pretty sufficient statistics for the underlying problem.
-
- changed status to resolved
- Log in to comment