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

[Vojtěch Zeisek]

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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