[adegenet-forum] Fst values

[Jombart, Thibaut]

Hi there,

for 1) please check the manpage - "pop" is there to specify populations!

As for 2), it is hard to find out without knowing how NJ155_gen has been created. This should be a genind object, with something in @pop as you leave pop=NULL. A minimal reproducible example would be useful.

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 Tara Baris [tzbaris at icloud.com]
Sent: 20 November 2014 17:13
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Fst values

Hi,

I’m trying to calculate Fst values for about 10,000 loci in two different populations using the following line of code:

 pairwise.fst(x, pop=NULL, res.type=c("dist","matrix"), truenames=TRUE)

I have two questions:

1) How would I specify the populations in this line? If I included a population definition file when converting to a genetix file, is that sufficient, and would the it still be pop=NULL?

2) When I try to run this in R, I get the following error message. Am I missing something?

> pairwise.fst(NJ155_gen, pop=NULL, res.type=c("dist","matrix"), truenames=TRUE)

Error in sub(paste("^.{", ncode/ploidy, "}", sep = ""), "", X) :
  invalid regular expression '^.{543}', reason 'Invalid contents of {}’


Thank you,

Tara
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