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Hello,

I would like to estimate the clustering coefficient using the package syntenet as decribed here https://doi.org/10.1073/pnas.1801757116. Is there a function in the syntenet package to do that?

thanks Alex

Also how is this calculated exactly? From what I understand it is a measure of the quality of the blocks?

Hi, Alex

There's a function in cogeqc, another package of mine, that calculates quality scores for synteny networks (see this section in the vignette).

To understand the rationale for using such scores, I'd suggest taking a look at the preprint describing cogeqc, available here.

Best,

Fabricio

Dear Fabricio,

Many thanks for your reply. After checking the vignette and the preprint, it is still not entirely clear to me how the clustering coefficient is calculated and what it represents (no formula or explanation provided). The only info I found is that there is a trade-off between a good clustering coefficient and the number of nodes. I assume it represents how well the nodes are interconnected within the clusters?

Thanks Alex