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dipetkov / eems

Estimating Effective Migration Surfaces
GNU General Public License v2.0
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How about treat individuals from one location as a population? #54

Closed willright28 closed 2 years ago

willright28 commented 3 years ago

Hi all According to eems's manual this software is a individual-based approach to simulate the genetic dissimlarity between pairs, but if we access samples from the same geographical location to a population and simulate difference between those population, will it influence the result? For example, if I got 100 samples from 10 locations, then I will calculate a pop's genetic dissimlarity matrix with dim 10 by using other software, and run eems by setting nIndiv to 10. I'm totally awaring of how bad this question is, however I have to have a try for some terrible reasons. And what's more terrible is that eems gave error information 'matrix is not a full-rank matrix' when I implemented it, but I can not find why.. I really appreciate it if someone could convince me it's a stupid idea to do that! Thanks in advanced!

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dipetkov commented 3 years ago

With individual-level data we get to see how dissimilar individuals in the same deme/location are to each other compared to individuals in other demes. With population-level data we don't have information about dissimilarities within demes.

And the "full-rank distance matrix" check makes sure the matrix of genetic dissimilarities is a proper distance matrix. (Otherwise the math doesn't work out.)

dipetkov commented 3 years ago

Your question reminded me of a previous question about using the matrix of F_{ST}s as input. You can read more about this in the folder "Pairwise_FSTs".

willright28 commented 3 years ago

Thanks for your reply，I will check the folder

---Original--- From: "Desislava @.> Date: Sun, Aug 8, 2021 08:03 AM To: @.>; Cc: @.**@.>; Subject: Re: [dipetkov/eems] How about treat individuals from one location as a population? (#54)

Your question reminded me of a previous question about using the matrix of F_{ST}s as input. You can read more about this in the folder "Pairwise_FSTs".

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