[adegenet-forum] question regarding error for mantel.randtest

Yadav-Pauletti, Sunita (yadavps) yadavps at mail.uc.edu
Fri Dec 12 16:18:49 CET 2014

Hello Thibaut,

Thank you for your suggestion. The code I used was looking at overall object sizes and not matrices so I could see that Dgen and Dgeo were different sizes but not why.
The issue seems to be that Dgen (genetic) matrix is a 7x7 matrix - populations, and Dgeo (geographic) is a 241x241 - individuals. I would like to test IBD both at the population level and individual level (within populations). For populations, can I get geographic distances in adegenet or should I calculate it in my GIS software and read the distances? Secondly, can the following code be used for individual genetic distances in adegenet? It seems to work and I could run the mantel test.

Dgen <- dist(genfile, method="euclidean")
Dgeo <- dist(genfile$other$xy, method="euclidean")

The genAlEx file format is the following, data starts at row 4:
Individual_ID       Pop_ID     Alelle_1    Allele_1b   ......  Blank Column    X               Y
951_gps22          951          187            187           ......                          748600      2326728

The next question I have is how I can incorporate distances from a friction surface (cost surface) for a mantel test. Is there a way to read those distances in adegenet?


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