PCA of 23andMe data from openSNP + HapMap

A simple PCA plot done with ~1400 23andMe data sets found on openSNP + the HapMap data. A list of ~100 Ancestry Informative Markers, from http://www.biomedcentral.com/1471-2156/10/39, was used for the PCA. Data mangling was done using PLINK. PCA was run with smartpca, without any optimizing for outliers. Plotting done with R + ggplot2. HapMap population keys can be found here: https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html

本数据集基于公开基因组数据平台openSNP上获取的约1400条23andMe基因数据集，结合国际人类基因组单体型图计划（HapMap）数据，绘制了一幅简易主成分分析（Principal Component Analysis, PCA）可视化图。本次分析采用了约100个祖先信息标记（Ancestry Informative Markers），其来源为文献http://www.biomedcentral.com/1471-2156/10/39。数据规整工作借助PLINK工具完成。主成分分析通过smartpca软件运行，未针对异常值进行优化处理。可视化绘图使用R语言及ggplot2包完成。HapMap群体分组标识文件可通过以下链接获取：https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html