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

[Thibaut Jombart]

Hi,

what you describe sounds like a complete linkage clustering. What you wanna
do is:

1) get hamming distances using dist.dna (you got that already)
2) use hclust specifying the right method for complete linkage clustering
3) use cutree on the resulting dendrogram for a given threshold

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
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Twitter: @TeebzR <http://twitter.com/TeebzR>
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On 10 January 2017 at 13:39, Hiren Ghosh <hiren.ghosh at gmail.com> wrote:

> 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
>
>
>
>
>  Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh@gmail.com&idSignature=22>
>
> 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
>>
>>
>>
>>  Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh@gmail.com&idSignature=22>
>>
>> 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>
>>>
>>>
>>>
>>>  Sent with Mailtrack
>>> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh@gmail.com&idSignature=22>
>>>
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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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