[adegenet-forum] glPlot: which sample is used as the reference?

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Jan 15 16:42:41 CET 2015

Hi there, 

I suspected this misunderstanding. genlight stores biallelic data are coded as binary, so the first allele is 0 and the second is 1 for all sites, the definition of first and second being arbitrary.

From: Yan Hou [yan.hou at nhm.uio.no]
Sent: 13 January 2015 19:27
To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference?

Thanks a lot for your reply! I am sorry, but I might do not describe my
question clearly.

My question is: which sequence was chosen as the reference when using
the glPlot?

The plot implies the existence of a reference sequence (i.e. a missing
site in relation to what? A SNP in relation to what?), right?



On 13.01.2015 18:58, Jombart, Thibaut wrote:
> Hi there,
> individuals are plotted according to their order in the genlight object
> (individuals' indices are indicated on the y-axis.
> Cheers
> Thibaut
> ------------------------------------------------------------------------
> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org
> [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan
> Hou [yan.hou at nhm.uio.no]
> *Sent:* 12 January 2015 21:26
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Cc:* Yan Hou
> *Subject:* [adegenet-forum] glPlot: which sample is used as the reference?
> Hi,
> I managed to use glPlot( SNPs,posi="topleft" ) to present the position
> of SNPs in my concatenated and aligned RAD-seq data matrix. When looking
> at the figure, I wonder which sample was used as the reference? The
> first sample in the input file or the sample with most complete sequence
> data? My first sample has a large number of missing data, so I wonder?
> Cheers,
> Yan

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