I know that there are quite a few packages out that there for cluster
analysis.  The problem that I am facing is finding a package that will not
incorporate all my samples into clusters but just the samples that fit a
threshold (that I have not set yet and may need help finding the right
level) for genotyping. It should be able to "no call" samples outside the
clusters. It also needs to accommodate a negative control sample by not
including it in any genotype cluster.

I'm looking at both nuclear and mitochondrial DNA so hopefully it can be
sophisticated enough to set the number of cluster between two or three
within the array.

These genotyping arrays are either 48 samples x 48 assays, 96x96, or 192x24
and it would be nice if it could accommodate any range of samples and
assays.

the data headings from the csv are:

ID,Assay,Allele Y,Allele X,Name,Type,Auto,Confidence,Final,Converted,Allele
Y,Allele X

where Allele Y and Allele X are the plotted values and the vectors within
the data.frame are 9216 (96x96) long.

So what would be the recommended package for moving to a more quantifiable
method of genotyping using cluster analysis?

Thanks again.  I will provide any additional context that I might have
forgot to add here that could help.

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