I have a table with pairwise doubleton allele sharing counts, and I am trying to run a PCA on my results
Sample1 Sample2 Sample3 Sample4 Sample5 Sample1 - 7 13 4 13 Sample2 7 - 2 15 8 Sample3 13 2 - 11 10 Sample4 4 15 11 - 5 Sample5 13 8 10 5 -
Each value in the able corresponds to the number of doubleton SNPs shared by the corresponding samples (all the samples were made pseudohaploid, so doubletons are always shared between exactly two samples).
I need to run a PCA on these results, and I am a bit lost. I was wondering if anyone has any suggestions on how I can do this.