PCA projection - strange population classification

Question

PCA projection - strange population classification

numicator opened this issue 4 years ago · comments

Hi,

I am analyzing a kindred - two parents and two kids. The PCA projection of the samples is attached below. Mother is the sample of clearly EU ancestry, PC2 ~ -1.5, Father is in my opinion of clear SAS ancestry, PC2 ~ -0.4, The children are the two dots in between. As you can see from the PC1/PC2 plot, the father looks pretty much SAS. Peddy classified all samples as of EU ancestry. Why is it so?

Brent Pedersen · Answer 1 · Mon Apr 20 2020 22:09:25 GMT+0800 (China Standard Time)

hmm, that is an odd one. this can happen some times. there is a 4th dimension, not plotted that the svm uses to cluster as well. i will be working on improving ancestry classification over the next few weeks in somalier -- but that is not accurate yet, for cases like this one.

numicator · Answer 2 · Wed Apr 22 2020 19:59:59 GMT+0800 (China Standard Time)

yap, it's a strange one. Seems individual of mixed ancestry. BTW, are you planning further active development of peddy or shifting to somalier?

Brent Pedersen · Answer 3 · Wed Apr 22 2020 20:50:41 GMT+0800 (China Standard Time)

peddy is stable, but I will continue to fix any bugs that arise. other than that, I will focus more on somalier.