Cluster analysis for SNPs data in R

Question

[misterie]

Hi everyone.

I have a question. I have 4 SNPs data which represents 4 cattle breeds. I need to do comparison this SNPs so I need use a cluster analysis. The data looks like: CHROMOSOME (1st column), POSITION (2nd column), NUCLEOTIDE e.g. A/G (3rd columns).

Could help me, how to make a cluster analysis in R package.

Thank you in advance, Bartosz

[al]

There are some general approaches here Snp Cluster Analysis and here How To Make A Phylogenetic Tree From A Binary Matrix

If it is a dendrogram you're after, then something quite close to your set-up ('Simple SNP File Format') using phylip/phangorn is described here http://chibba.pgml.uga.edu/snphylo/ A bespoke approach using the ggdendro package is also possible.