[R-sig-genetics] Microsatellite data query: Data frame to genind conversion using adegent in R

[Bhuller, Ravneet]

Dear Thibaut and Vojtec,

Everything is working fine now.

Many thanks for the great guidance.

Rav





> On 9 Dec 2016, at 11:50, Vojtěch Zeisek <vojta at trapa.cz> wrote:
> 
> Dne pátek 9. prosince 2016 11:33:21 CET, Bhuller, Ravneet napsal(a):
>> Hello R-sig-genetics community members,
>> 
>> I am using microsatellite data for the first time. It is in csv format.
>> Individual ids (1314 in total) are in the first column of the file (a
>> snapshot attached below) and the allelic information of each loci (17 loci)
>> is in duplicate columns.
>> [cid:F92F6AA3-0C16-4642-843F-476A5B1D6839 at nhm.ac.uk]
>> 
>> When I convert this data.frame into genind object using adegent, it is
>> considering first column as a locus and calculates number of loci as 35
>> (see below): [cid:423CE768-65F3-4B01-9E38-63CA0FD5ABF1 at nhm.ac.uk]
>> 
>> Please if anyone can guide me what is going wrong here. The actual number of
>> loci is 17 and first column is not a locus.
> 
> Hi,
> it is well documented in the Adegent basics tutorial. Mine shortened version 
> is in https://trapa.cz/en/course-molecular-data-r-2016 (see PDF attachment 
> down the page from slide 42).
> HTH,
> V.
> 
> -- 
> Vojtěch Zeisek
> https://trapa.cz/en/
> 
> Department of Botany
> Faculty of Science, Charles University
> Benátská 433/2, Prague, 12801, CZ
> https://www.natur.cuni.cz/biology/botany/
> 
> Institute of Botany, Academy of Sciences
> Zámek 1, Průhonice, 25243, CZ
> http://www.ibot.cas.cz/en/
> 
> Czech Republic
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