June 2015
Intermediate to advanced
306 pages
6h 50m
English
Content preview from Bioinformatics with Python CookbookBecome an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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Performing Principal Components Analysis
Principal Components Analysis (PCA) is a statistical procedure to perform a reduction of dimension of a number of variables to a smaller subset that is linearly uncorrelated. Its practical application in population genetics is assisting the visualization of relationships of individuals that is being studied.
While most of the recipes in this chapter make use of Python as a "glue language" (Python calls external applications that actually do most of the work) with PCA, we have an option, that is, we can either use an external application (for example, EIGENSOFT smartpca) or use scikit-learn and perform everything on Python. We will perform both.
Getting ready
You will need to run the first recipe in order ...
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