[adegenet-forum] find.clusters() freezes on DAPC

[Thibaut Jombart]

Hi,

it is probably not stuck, it asks you for a number of PCs to retain.

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: https://repidemicsconsortium.org
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 1 October 2016 at 22:30, Alan Garcia-Elfring <alangarcia87 at hotmail.com>
wrote:

> Hi everyone,
>
>
> I'm wondering if anyone has gotten stuck on the find.clusters function?
>
>
> I did a DAPC on this exact dataset in some months back and now I want that
> I redo it to check a different K value and change the colours, but it keeps
> getting stuck on find.clusters.
>
>
> Any idea what may be causing this? If I remember correctly, this step
> doesn't take long, definitely not more than a day.
>
>
> I've tried on a new mac and also on a PC using the parallel = FALSE
> argument.
>
> Any help is appreciated.
>
> >pldata = read.PLINK("batch_1_recode.raw")
>
> >grp = find.clusters(pldata, max.n.clust = 15)         ##GETS  STUCK ON
> THIS
>
>
>
> /// GENLIGHT OBJECT /////////
>
>  // 229 genotypes,  62,236 binary SNPs, size: 15.3 Mb
>
>  // Basic content
>    @gen: list of 229 SNPbin
>    @ploidy: ploidy of each individual  (range: 2-2)
>
>  // Optional content
>    @ind.names:  229 individual labels
>    @loc.names:  62236 locus labels
>    @pop: population of each individual (group size range: 8-20)
>    @other: a list containing: sex  phenotype  pat  mat
>
>
>
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