Illumina analysis and partitiona around medoids

I have included a couple of lines in the draft package to define the
scores variable as just the mutations identified by the illumina Hi-seq.
I have also included code at the bottom for creating metric MDS plots
colored according to PAM cluster assignment. I can also color non-metric
MDS plots according to PAM cluster assignment. I am currently looking
for a function to create self-organising maps based on binary data.