[adegenet-forum] SNP data

Thibaut Jombart thibautjombart at gmail.com
Wed Jul 12 16:25:44 CEST 2017

Hi there

there are different ways you can go about this. If RAM isn't an issue, and
some loci have more than 2 alleles, then you can use df2genind on a
data.frame where alleles are coded with letters separated by a character,
e.g. "a / t / a / g", or even "atag", i.e. no separator but you'll need to
specify the n.char argument.

If RAM is an issue, genlight will let you store information on polyploids
(see the tutorial on 'genomics'). The input would be a matrix of integers,
each representing the number of the 2nd alleles (indiv in rows, SNPs in


Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
Twitter: @TeebzR
+44(0)20 7594 3658

On 30 May 2017 at 20:06, Weiya Xue <wxx10 at psu.edu> wrote:

> Hi ,
> I want to use adegenet for SNP data analysis in ployploids. How should I
> prepare the data?
> Does any one have the syntax of the input file?
> Thanks,
> Weiya Xue
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