[adegenet-forum] Query about Adegene : How to get snp position plateau curve

[Hiren Ghosh]

My data set like this : I have a core genome alignment of 240 e coli
genome, which are varying number of snps from ~0-44200. Now i would like to
clustered  all them according to number of snps. Suppose all the genome
share bellow 100 snps will be one cluster so on all bellow 500 will be one
cluster so on.....
Can anyone suggest some idea. how to proceed.
Thanks




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On 10 January 2017 at 13:43, Roman Luštrik <roman.lustrik at biolitika.si>
wrote:

> Forwarding this to the list.
>
> It's not clear to me what you would like to measure. Would like to see,
> given a constant cutoff, when clusters don't change much as you add SNPs?
>
> Cheers,
> Roman
>
>
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
> *To: *"Roman Luštrik" <roman.lustrik at biolitika.si>
> *Sent: *Tuesday, January 10, 2017 1:33:52 PM
> *Subject: *Re: [adegenet-forum] Query about Adegene : How to get snp
> position plateau curve
>
> Hello,
> I am very new to such analysis. Mainly my aim is to cluster based on the
> number of mutations separating sequences, classifying them in the same
> cluster if their distance is less than a given threshold.
> Thanks For reply.
> Kind
> Hiren
>
>
>
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>
> On 10 January 2017 at 13:25, Roman Luštrik <roman.lustrik at biolitika.si>
> wrote:
>
>> What statistic are you trying to square off against number of SNPs?
>>
>> Cheers,
>> Roman
>>
>> ----
>> In god we trust, all others bring data.
>>
>> ------------------------------
>> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
>> *To: *adegenet-forum at lists.r-forge.r-project.org
>> *Sent: *Tuesday, January 10, 2017 12:04:25 PM
>> *Subject: *[adegenet-forum] Query about Adegene : How to get snp
>> position        plateau curve
>>
>> Hello Developer, Currently i am using your adegent package,  in this way :
>> #data input from multi-genome-alignment file
>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")
>> D <- dist.dna(dna, model="N")
>> clust <- gengraph(D)
>>
>>
>> I would like to have a look how many snps position is there until my data
>> will be a plateau curve.  . Could you please help me out.
>>
>>
>> Thanks Advance.
>>
>>
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches
>> Forschungszentrum SeltersbergInstitut für Medizinische
>> MikrobiologieJustus-Liebig-UniversitätSchubertstr. 8135392 Gießen , Germany*
>>
>> *Mobile No: 017672157634*
>>
>> *Email:hiren.ghosh at med.uni-giessen.de*
>> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>>
>>
>>
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>
>
>
> --
>
>
>
>
>
>
> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
> SeltersbergInstitut für Medizinische
> MikrobiologieJustus-Liebig-UniversitätSchubertstr. 8135392 Gießen , Germany*
>
> *Mobile No: 017672157634*
>
> *Email:hiren.ghosh at med.uni-giessen.de*
> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>
>


-- 






*Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
SeltersbergInstitut für Medizinische
MikrobiologieJustus-Liebig-UniversitätSchubertstr. 8135392 Gießen , Germany*

*Mobile No: 017672157634*

*Email:hiren.ghosh at med.uni-giessen.de*
<Email%3Ahiren.ghosh at med.uni-giessen.de>
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