[adegenet-forum] I: HWE

[Carlo Pecoraro]

Hi all,

I am trying to remove from my dataset those loci in HWE. I have measured it both per population: hwe.pop<-(lapply(seppop(x), hw.test) and per locus hwe.loc<-hw.test(x), B=1000).
Now I would like to define a threshold (0.05) for the Pr(chi^2>), removing all those loci with a derived P-values above this threshold. How could I perform this analysis? Do you have any suggestion?

I am wondering if this is the best way to filter my dataset according to the HWE. Any advise would be more than welcome.

Best regards,
Carlo


Da: Carlo Pecoraro
Inviato: lunedì 17 agosto 2015 16:14
A: 'adegenet-forum at lists.r-forge.r-project.org'
Oggetto: HWE

Hi all,

I am trying to remove from my dataset those loci in HWE. I have measured it both per population: hwe.pop<-(lapply(seppop(x), hw.test) and per locus hwe.loc<-hw.test(x), B=1000).
Now I would like to define a threshold (0.05) for the Pr(chi^2>), removing all those loci with a derived P-values above this threshold. How could I perform this analysis? Do you have any suggestion?

I am wondering if this is the best way to filter my dataset according to the HWE. Any advise would be more than welcome.

Best regards,
Carlo
--

Carlo Pecoraro, PhD Candidate

Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM)
Dept. Biological, Geological & Environmental Sciences (BiGeA)
University of Bologna
Via S. Alberto 163, 48123 Ravenna (Italy)

IRD (Institut de Recherche pour le Développement)
UMR 212 EME (Ecosytèmes Marins Exploités)
BP 570
Victoria, Mahé
Seychelles

Ph: +39 3337603101
skype contact: carlo_pecoraro

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