Closed beausoleilmo closed 1 year ago
Hi,
Yes everything is correct. For your last point, the estimates of observed and expected heterozygosity is not outputted unfortunately and only summarized by F. Here F is 1 - obs(het)/exp(het) accounting for population structure using individual allele frequencies as defined in https://doi.org/10.1111/1755-0998.13019.
Best, Jonas
OK thanks!
In the README, it says that PCAngsd can "PCAngsd can perform the following analyses: HWE test".
But I don't see an option that can do that.
So far I have
The in R
So:
Is everything correct here? Where are the estimates of observed vs expected heterozygosity?