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Cluster Lines by Genotype

This R program will cluster the currently selected lines according to their alleles for all markers, using "pam" (Partitioning Around Medoids). Analysis code VisualCluster.R.

The results will be displayed as a two-dimensional PCA plot with the clusters color-coded. If you enter some line names below, the legend will indicate which cluster they fall into.

When you have examined the results you can select the clusters you want to work with.

How many clusters should pam divide the lines into?    (Maximum 8.)

Lines to label in the legend:
E.g. MERIT, FEG148-16, ND24205, VA07B-54

Minimum MAF ≥ %      Remove markers missing > % of data      Remove lines missing > % of data     

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement

I agree to the Data Usage Policy as specified in Toronto Statement.