[adegenet-forum] Importing rowwise SNP data into adegenet [SEC=UNCLASSIFIED]

[Thibaut Jombart]

Hello,

This format is quite different from what adegenet can currently read. I
haven't played with such data much so not in the best position to comment,
but it looks like this might be a plink-friendly format? In which case you
could convert these to plink and read them into R using
adegenet::read.PLINK ? Alternatively if you can get sequences, read them
into R from a fasta file and then extract the polymorphism from there (all
documented in basics tuto).

Cheers
Thibaut


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

On 3 May 2018 at 07:13, Dale Maschette <Dale.Maschette at aad.gov.au> wrote:

> Hello All,
>
> I have recently been sent some SNP data in CSV and am trying to work out
> how to get it imported with adegenet.
>
>
>
> The data is samples as columns and alleles as rows because the full
> dataset has more alleles than CSV can handle as columns. I have read the
> tutorials and documentation but can’t seem to work out if it’s possible.
>
>
>
> I have attached an example data set, if anyone could suggest how to import
> it I would be very grateful.
>
>
>
> Cheers,
>
> Dale
>
>
>
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