[adegenet-forum] snapclust and genlight

[Thibaut Jombart]

Hi there,

this is a technicality: given the internal data structure of genlight
objects, a native implementation of snapclust for these objects would be a
lot of (hard) work. genlights are only really useful when genind cannot be
used (not enough RAM).

In terms of doc, I hear what you say, but as you pointed out the
documentation already says genind objects are expected as inputs. Where
else would you recommend we specify this?

Cheers
Thibaut

--
Dr Thibaut Jombart
Associate Professor in Outbreak Analytics, London School of Hygiene and
Tropical Medicine
Senior Lecturer in Genetic Analysis, Imperial College London
President of RECON: repidemicsconsortium.org
https://thibautjombart.netlify.com
Twitter: @TeebzR


On Mon, 22 Oct 2018 at 14:33, Pfau, Dr. Russell S. <PFAU at tarleton.edu>
wrote:

> Hi all,
>
> For snapclust, it appears that it only reads genind objects and not
> genlight objects. This wasn’t mentioned in the tutorial, but I see this
> specified in the adegenet manual:
>
> Usage snapclust(x, k, pop.ini = "ward", max.iter = 100, n.start = 10,
> n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL,
> parent.lab = c("A", "B"), ...)
>
> Arguments
>
> x a genind object
>
> https://cran.r-project.org/web/packages/adegenet/adegenet.pdf
>
>
>
> Given that genlight and snapclust (I think) were both developed primarily
> for large snp datasets, that doesn’t make sense to me. I assumed snapclust
> would use genlight objects, and it took me a while to realize otherwise. It
> might help others to clarify.
>
>
>
> Thanks,
>
> Russell
>
>
>
> <+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+>
>
>
>
> Russell S. Pfau, PhD
>
> Professor, Department of Biological Sciences
>
>
>
> Biological Sciences Box T-0100
>
> Tarleton State University
>
> Stephenville TX 76402
>
>
>
> 254-968-9761
>
>
>
> http://faculty.tarleton.edu/pfau/
>
>
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