Plink: Creating Dendrograms Of Ibs Clustering Solutions
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10.9 years ago
bdeonovic ▴ 210

If I have the full solution path for IBS clustering from PLINK e.g.:

 A 1 0 0 0 0
 B 1 1 1 1 0
 C 1 2 1 1 0
 D 1 3 2 0 0

Where first column is family ID, second column is sample ID and the rest of the columns are solution path of clustering (i.e. every step of the clustering from moving from N clusters each of 1 individual (leftmost column after family and individual ID) to 1 cluster (labelled 0) containing all N individuals (the final, rightmost column))

How can I make a dendrogram of this. For the example it should look something like this:

http://pngu.mgh.harvard.edu/~purcell/plink/tree1.png

plink clustering • 5.2k views
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Thanks for the links, good packages. I decided to use the R package SNPRelate, which is amazing for working with SNP data

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