[adegenet-forum] Reading a genepop file with adegenet

Thibaut Jombart thibautjombart at gmail.com
Mon Apr 24 17:06:11 CEST 2017


upon inspection, I think your file is corrupt - there are two rogue
'00000000' (8 times 0). After replacing these and specifying ncode = 3 it
reads fine.


Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
Head of RECON: repidemicsconsortium.org
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 24 April 2017 at 15:32, Robert Fairweather <rb951092 at dal.ca> wrote:

> Dear Forum,
> I am having some trouble importing my genepop file into adegenet using the
> read.genepop function. I have set the ncode argument to 3 to reflect the
> the character format of my SNP data (eg 001003) but still receive the error
> "some alleles are not encoded for by three characters"
> The error persists even with the default ncode parameter and a two
> character format used. Missing data is coded for as 000000 (or 0000 in 2
> character format) and upon comparison with the nancycats file I cannot see
> any differences. Are you able to help me out? I have attached the file.
> Many thanks,
> Robert
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