[adegenet-forum] Find clusters on distance matrix or relative frequency.

Francesco Montinaro francesco.montinaro at gmail.com
Fri Jul 19 19:22:30 CEST 2013

I have a matrix very similar to Structure/ADMIXTURE output but produced
with a local ancestry algorithm.

For example for each population (10 populations) I have how much it
"copies" from each of the other populations. Visually,It seems that there
are 2 main clusters in composition of each populations, so I would like to
cluster them.
Unfortunately my matrix is based on relative proportion, and I am afraid
that find.cluster function is not suitable because it uses PCA. I was
thinking to use the distance matrix of my original data, but I am not sure
that it is mathematically correct.

In addition I would like to know the right number of cluster, so I cannot
use kmeans, not natively at least.

Do you have any suggestion?

Thank you for your help.

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