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

[Yan Hou]

Thanks a lot! It is very clear now. Yan

On 28.01.2015 15:20, Jombart, Thibaut wrote:
>
> 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
>>
>