[adegenet-forum] Treatment of ploidy by seploc

[Jombart, Thibaut]

Hello, 

this was a documented bug, which has now been corrected. 

Why use seploc ("separate loci") if you have one locus? 

Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Aaron.Adamack [Aaron.Adamack at canberra.edu.au]
Sent: 05 August 2013 08:14
To: 'adegenet-forum at lists.r-forge.r-project.org'
Subject: [adegenet-forum] Treatment of ploidy by seploc

Hi Thibaut,
I’m working on building a function that uses the seploc function on a tetraploid genind object that has a single microsatellite locus with two alleles (e.g. A and B). I’m a bit puzzled by the function’s behaviour....

If I have a genind object called “example” and type:
>example at ploidy
The output is:
>4

However if I try:
>seploc(example)[[1]]@ ploidy
I get:
>2

Why would the ploidy change if I separated the loci (just as a note in case it’s not obvious, this is just a test case)? I obtained the same result when I duplicated the locus and repeated these steps (checking to see if it might have been due to running seploc on an individual with only one locus). I obtained a similar result when I tried seploc on genind objects with initial ploidies of 3 and 6. In the initial step I got ploidies = 3 or 6 and in the second step I got ploidy = 2.

Thanks for the help,
-Aaron