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

[Yan Hou]

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
>