[adegenet-forum] How we can convert the genotyping result of SSR marker to binary cod

[Roman Luštrik]

The function `read.genepop` does that for you. You didn't provide a fully working genepop example, but here's a demonstration using nancycats dataset: 

> xy <- system.file("files/nancycats.gen", package = "adegenet") 
> system(sprintf("cat %s", xy)) 
Genotypes of cats from 17 colonies of Nancy (France) 
fca8 
fca23 
fca43 
fca45 
fca77 
fca78 
fca90 
fca96 
fca37 
Pop 
1, 0000 0409 0404 0103 0909 0306 0909 0808 1010 
1, 0000 0909 0407 0305 0909 0306 0209 0808 1010 
1, 0913 0409 0505 0101 0709 0303 0808 0808 1111 
1, 0809 0505 0405 0105 0606 0306 0909 0104 1010 
... 

> xy <- read.genepop(xy) 
... 

> tab(xy)[1:10, 1:10] 
fca8.09 fca8.13 fca8.08 fca8.10 fca8.12 fca8.06 fca8.07 
001 NA NA NA NA NA NA NA 
002 NA NA NA NA NA NA NA 
003 1 1 0 0 0 0 0 
004 1 0 1 0 0 0 0 
005 1 0 1 0 0 0 0 
006 1 1 0 0 0 0 0 
007 2 0 0 0 0 0 0 
008 1 1 0 0 0 0 0 
009 0 1 0 1 0 0 0 
010 2 0 0 0 0 0 0 

Is this what you're after? 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 
> Zahtevaj IJZ na https://kurc.biolitika.si 


From: mbzandi at znu.ac.ir 
To: adegenet-forum at lists.r-forge.r-project.org 
Cc: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, May 22, 2017 10:33:54 PM 
Subject: Re: [adegenet-forum] How we can convert the genotyping result of SSR marker to binary cod 

Dear all, 
I am a new member of this forum, I’m trying to use adegenet to define genetic clusters and genetic diversity between two groups. 
As mentioned in user guide the SSR data converted to binary code like "data(microbov)". I have raw genotyping result in Genepop format as copied below: 

============================ 
pop 
77568 , 0308 0506 0205 0404 0405 0105 0103 0405 0406 0103 0505 0506 0306 
77571 , 0108 0104 0207 0607 0505 0202 0505 0101 0104 0104 0606 0404 0108 
77575 , 0103 0102 0608 0104 0210 0203 0202 0103 0406 0404 0202 0406 0104 
77579 , 0303 0102 0407 0406 0405 0203 0305 0107 0406 0103 0505 0405 0304 
77580 , 0104 0105 0105 0406 0305 0304 0305 0203 0202 0303 0606 0405 0304 
.... 
===================================== 
My question is: How I can convert the genotyping result of SSR marker to binary code in adegenet? 
Is it possible with other packages or other software in this regards? 

Has anyone come across this and be able to overcome it? 

Best regards, 
Mohammad 


================================== 
Mohammad Bagher Zandi B.M. 
Genetics and Animal Breeding(PhD) 
Associate Professor 
Faculty of Agriculture 
Department of Animal Science 
University of Zanjan, Zanjan, Iran 


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