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

[Roman Luštrik]

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 Seltersberg 
Institut für Medizinische Mikrobiologie 
Justus-Liebig-Universität 
Schubertstr. 81 
35392 Gießen , Germany 

Mobile No: 017672157634 

Email:hiren.ghosh at med.uni-giessen.de 



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-- 


Hiren Ghosh, Doctoral Research Scholar 
Biomedizinisches Forschungszentrum Seltersberg 
Institut für Medizinische Mikrobiologie 
Justus-Liebig-Universität 
Schubertstr. 81 
35392 Gießen , Germany 

Mobile No: 017672157634 

Email:hiren.ghosh at med.uni-giessen.de 

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