[adegenet-forum] Fst for mitochondrial DNA

[Jombart, Thibaut]

Hello, 

It looks like some positions are missing for at least one population, resulting in a NA for the Fst.

Cheers

Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Stefan Prost [stefan.prost at anatomy.otago.ac.nz]
Sent: 30 January 2013 04:54
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Fst for mitochondrial DNA

Hello,

 I would like to calculate Fst's for 25 populations (all in all about 1200
complete mitochondrial genomes). I used the pairwise.fst function from
adegenet, but got NA's in the results and warnings

In df2genind(tab, pop = pop, ploidy = x[[1]]@ploidy, type = x[[1]]@type) :
 entirely non-type marker(s) deleted


All sequences should be ploidy 1 and type codom.

Any ideas why it calculates the FST for some, but by far not all
populations? Is that a data input problem or something else?

Thanks for the help!

Best,
Stefan

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