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

[Alan Garcia-Elfring]

Nevermind!

Finally got it to work on the mac, although the optimal K changed when assessing different ranges of K.

(Hopefully when I redo it with the original range of K I will get the same optimal K as I'm getting ready to publish!)


Cheers

Alan

________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org <adegenet-forum-bounces at lists.r-forge.r-project.org> on behalf of Alan Garcia-Elfring <alangarcia87 at hotmail.com>
Sent: 01 October 2016 17:30
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] find.clusters() freezes on DAPC


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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