Cluster analysis for SNPs data in R
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
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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.