Optimal core set size

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Ira Herniter

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Apr 29, 2025, 10:51:40 AMApr 29

to Core Hunter Users

Hi,

I'm using the R package for corehunter to identify a core collection. I see that running corehunter requires you to specify the end size of your core set. Is there a way to optimize the size without simply running it repeatedly with the size set to different numbers?

-Ira

Herman De Beukelaer

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Apr 30, 2025, 8:58:02 AMApr 30

to Core Hunter Users

Hi Ira,

Core Hunter does not optimize across sample sizes. In my experience, it is also difficult to compare the metrics across samples of different sizes. The different metrics typically increase (e.g. allele coverage) or decrease (e.g. genetic distance measures) when the core set size increases. So what kind of optimum are you looking for?

Herman

Op dinsdag 29 april 2025 om 16:51:40 UTC+2 schreef iher...@gmail.com:

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