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

[Jombart, Thibaut]

I don't know how to rephrase my previous reply more explicitly. 

The choice of the 'reference' SNPs is arbitrary. There is no reference sequence used, but the one implied by the coding is arbitrary.

Cheers
Thibaut
________________________________________
From: Yan Hou [yan.hou at nhm.uio.no]
Sent: 27 January 2015 13:52
To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference?

Hi,
Thanks a lot for your explanation! So, the reference sequence was
arbitrary, right?

Cheers,

Yan


On 15.01.2015 16:42, Jombart, Thibaut wrote:
> 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.
>
> Cheers
> Thibaut
> ________________________________________
> 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?
>
> Hi,
> 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?
>
> Cheers,
>
> Yan
>
>
>
> 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
>