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Indian Cline
I had used linear regression to estimate Ancestral South Indian (ASI) component from Reference 3 K=11 admixture run. Now here are a couple more exercises along the same lines but much simpler. Just...
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Indian Cline II
One thing I forgot in the post yesterday about the Indian cline was to try to extrapolate from the PCA results to 100% ANI (Ancestral North Indian) and 100% ASI (Ancestral South Indian). This is a...
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Indian Cline III
I have been working on creating 100% ASI (Ancestral South Indian) samples recently. So it was really interesting that Dienekes did similar experiments: How to create Zombies from ADMIXTURE etc. More...
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Reference 3 + HAP PCA
I had run PCA on the Reference 3 dataset before. Now I included Harappa participants in it as well. Here's the dendrogram based on the Euclidean distance between Harappa participants in their PCA...
View ArticleReference 3 + Yunusbayev + HAP PCA and Mclust
I ran Principal Component Analysis (PCA) on reference 3 along with Yunusbayev et al Caucasus dataset and Harappa Ancestry Project participants (up to HRP0200). Then I ran mclust on the first 70...
View ArticleSouth Asian PCA + Mclust
I combined reference 3 with Metspalu et al data and Harappa Ancestry Project participants (up to HRP0200). Then I kept only those individuals whose combined proportion of South Asian and Onge...
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South Asian PCA Plots
I did a South Asian PCA + Mclust analysis last month. Here are the PCA plots from that analysis. First, the eigenvectors are not scaled to the eigenvalues in the plots. So here's a table explaining how...
View ArticleSouth Asian PCA 3D Plot
Here's a 3-D plot of my South Asian PCA run, showing the first three principal components. The principal components have been scaled according to their respective eigenvalues. The plot is rotating...
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ChromoPainter/fineStructure South Asians
You have probably heard of ChromoPainter/fineSTRUCTURE by now (Eurogenes, Dienekes, MDLP and Razib). So I decided to run the South Asian samples data which I had earlier done PCA/MClust on through...
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Dense South Asian ChromoPainter
I had run ChromoPainter/fineSTRUCTURE for 715 South Asians using only about 90,000 SNPs. I thought it would be a useful exercise to use more SNPs, so I had to drop the Reich et al dataset. That left me...
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