Question: PCA on pairwise allele sharing counts
1
gravatar for devenvyas
4 weeks ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

I have a table with pairwise doubleton allele sharing counts, and I am trying to run a PCA on my results

Example

        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.

snp pca • 101 views
ADD COMMENTlink written 4 weeks ago by devenvyas580
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