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Admixture Ref3 Dendrogram HRP0001-HRP0160
I haven't done any admixture dendrograms in a while, so I thought you guys might be interested. This uses admixture results using Reference 3. As usual, I used complete linkage for the hierarchical...
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...
View ArticleMetspalu Dataset Update
Dr. Metspalu, who has been very good about sharing data and information, has informed me about a couple of cases of mislabeling in the Metspalu et al dataset. Our sample labelled D238 and reported as...
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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...
View ArticleDodecad South Asian ChromoPainter
Dienekes ran ChromoPainter/fineSTRUCTURE analysis of South Asians along with some West Eurasian populations, something I had neglected to do in my own South Asian run. Using Dienekes' data, I was...
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Ref3 Admixture Dendrograms
I have posted the reference 3 K=11 admixture results for all populations and datasets. Here are the relevant links: Base Reference 3 Yunusbayev Metspalu Hodoglugil Xing Pan-Asian Henn Simonson Harappa...
View ArticleSouth Asian fineStructure Ref3 Admixture
I was wondering what the admixture patterns of the clusters fineSTRUCTURE computed were for my South Asian run. So I computed the average admixture for each cluster (total: 89) using reference 3...
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Eurasian fineStructure Dendrograms
The dendrogram in the last post about Eurasian ChromoPainter/fineStructure analysis is a little hard to make sense of, so here is the same info in a better format. First, the upper portion showing the...
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