Bioinformatics with Python Cookbook - Second Edition

See also

• The paper that probably popularized the use of PCA in genetics was Novembre et al., Genes mirror geography within Europe on nature, where a PCA of Europeans maps almost perfectly to the map of Europe. This can be found at http://www.nature.com/nature/journal/v456/n7218/abs/nature07331.html. Note that there is nothing in PCA that assures it will map to geographical features (just check our PCA earlier).
• The SmartPCA is described in Patterson et al., Population Structure and Eigenanalysis, PLoS Genetics, at http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020190.
• A discussion of the meaning of PCA can be found in McVean's paper on A Genealogical Interpretation of Principal Components Analysis, PLoS Genetics