I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is substantial structure in missing genotypes, shown here in a PCoA ordination of genotype matrix with 1-0 values, where 0 represents missing gt and 1 is presence of a gt value: Here the missingess threshold for genotype inclusion is <20%.
I want to cluster the samples using the scores on 20-30 PCoA axes, which is 17%-21% of variation, using the R package mclust. I ran
ape::PCoA() with an Euclidian distance matrix from
paralleldist::pardist(). When I run
mclust::mclustBIC(), I get a weird result in that the there is no modal value for any of the better-supported models, here shown in the legend:
I had expected to find a model that would support the existence of a small number of clusters (2-6 maybe). I also don't understand why the VVE model only has values to 3 clusters, where it presents the maximum value. Any ideas? I have tried relaxing the minimum missing level, and using data with differing minimum locus depth levels. I get very similar results.
Could someone please help me understand what is going on here and how I might address it? Once I have clusters, I can look at the assignment of samples to clusters by population, flowcell, and other stratifying variables. I would be happy to edit to include more information, if that would be helpful.