Tutorial to run PCA, Admixture, Treemix and pairwise Fst in one command
Today on Twitter I stated that “if the average person knew how to run PCA with plink and visualize with R they wouldn’t need to ask me anything.” What I meant by this is that the average person often asks me “Razib, is population X closer to population Y than Z?” To answer this sort […]
PCA remains the swiss-army-knife to explore population structure
genotype-based methods? — Razib Khan (@razibkhan) November 15, 2017 I put up a poll without context yesterday to gauge people about what methods they preferred when it came to population genetic structure.* PCA came out on top by a plural majority. More explicitly model-based methods, such as Structure/Admixture, come in right behind them. Curiously, the […]
Re-imagining genetic variation
To the left is a PCA from The History and Geography of Human Genes. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of gen…
The genetic world in 3-D
When Zack first mooted the idea of the Harappa Ancestry Project I had no idea what was coming down the pipe. I wonder if his daughter and wife are curious as to what’s happened to their computer! Since collecting the first wave of participants he…
D.I.Y. PCA
Long time readers know that I have a fixation on people not taking PCA too literally as something concrete. Tonight I finally merged the HGDP data set with some of the HapMap ones I’ve been playing with, and tacked my parents onto the sample. I…
Visualizing variation, input → output
I have noted a few times that one thing you have to be careful about in two dimensional plots which show genetic variance is that the dimensions in which the data are projected upon are often generated from the data itself. So adding more data can chan…
Just pushing buttons
Mike the Mad Biologist, whose bailiwick is the domain of the small, asks in the comments:
I don’t mean to bring up a tangential point to the post, but why does the field of human genetics use PCA to visualize relationships? When I see plots like those shown here that have a ‘geometric pattern’ to […]