Microsatellite data query: Data frame to genind conversion using adegent in R
Dne p?tek 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.
Vojt?ch Zeisek https://trapa.cz/en/ Department of Botany Faculty of Science, Charles University Ben?tsk? 433/2, Prague, 12801, CZ https://www.natur.cuni.cz/biology/botany/ Institute of Botany, Academy of Sciences Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part. URL: <https://stat.ethz.ch/pipermail/r-sig-genetics/attachments/20161209/4515d4f6/attachment.bin>