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You're reading from  Bioinformatics with Python Cookbook. - Second Edition

Product typeBook
Published inNov 2018
Reading LevelIntermediate
PublisherPackt
ISBN-139781789344691
Edition2nd Edition
Languages
Python
Tools
Biopython
Concepts
Bioinformatics
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Author (1)
Tiago Antao
Tiago Antao
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Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
Read more about Tiago Antao

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Performing Principal Components Analysis

PCA is a statistical procedure that's used to perform a reduction of the dimension of a number of variables to a smaller subset that is linearly uncorrelated. Its practical application in population genetics is assisting with the visualization of the relationships between the individuals that are 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: 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 to make use of the hapmap10_auto_noofs_ld_12 PLINK file (with alleles recoded as 1 and 2). PCA requires LD-pruned markers; we will not risk using the offspring here because it will probably bias the result. We will use the recoded PLINK file with alleles as...

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Bioinformatics with Python Cookbook. - Second Edition
Published in: Nov 2018Publisher: PacktISBN-13: 9781789344691
© 2018 Packt Publishing Limited All Rights Reserved

Author (1)

author image
Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
Read more about Tiago Antao

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