IBD (gl.ibd function): 'nperm' >= set of all permutations: complete enumeration error

[Sergio Bolívar]

Hi everyone,

I have problems implementing the gl.ibd function in o dataset of SNPs (28 samples, 3 pops, biallelic, 2036 loci).

The gl.ibd function shows the following message:

'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.

And the plot not shows all the data of my dataset (see figure).

I tried with other datasets (similar) and the function works fine (56 samples, 12 pops, biallelic, 1452 loci), and I am using the same version of the packages.

The number of population van be the problem?

Does someone have an idea of what could be the problem?

Thanks in advance!

[Bernd.Gruber]

Hi,

 

As you have only 3 populations (and currently gl.ibd is only running on populations) you have 3 pairwise Fsts and therefore the points are fine.

 

 

You also get the warning because the nperm setting of 1000 permutations cannot be done with 28 individuals there only the maximum number of permutations are performed in the mantel test.

 

If you want to do an isolation by distance on individuals you need a individual based distance e.g. 1-gl.propShared and then do your mantel test and plot “by hand”.

 

It is one of the things on my todo list to allow for individual and other distances.

 

Cheers, Bernd

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