[adegenet-forum] issues with genind object for MHC supertyping

[Anat Belasen]

Hello,

I have been trying to follow the example of many MHC studies that use DAPC
in adegenet to determine clusters/supertypes. According to what I've read,
I need to use a matrix of the physicochemical properties of the amino acids
in my MHC sequences to determine clustering. However, I can't get R to
accept this matrix as a genind object. I have been able to turn it into a
loci object but the loci2genind function returns an error:

Error in .local(.Object, ...) :
  more than one '.' in column names; please name column as [LOCUS].[ALLELE]

I have tried removing headers, changing the headers so they do resemble the
"locus.allele" format, and nothing seems to work. I'm not sure if this is
because this isn't a matrix of 0's and 1's (but rather values that include
decimals and sometimes are negative).

Can you advise how to proceed with this dataset? Perhaps is there an
example dataset used for this purpose?

Thank you,

Anat

-- 
-- 
Anat Belasen (personal website <https://anatbelasen.weebly.com/>)
M.S., Natural Resources and Environment 2013
<https://sites.google.com/a/umich.edu/foufopoulos/people/former-graduate-postgraduate-students>
PhD Candidate, Ecology & Evolutionary Biology
<http://www.umich.edu/~mycology/people.html>
FEMMES <http://femmes.studentorgs.umich.edu/> Secretary 2017-2018
University of Michigan
Ann Arbor, MI
@anatinmyshoe <https://twitter.com/anatinmyshoe>
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