Population Genomics with R

1st Edition

Emmanuel Paradis

Chapman and Hall/CRC
May 1, 2020 Forthcoming
Reference - 400 Pages
ISBN 9781138608184 - CAT# K388811

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Summary

Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies.

The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, methods seeking structure in population genomic data including supervised and unsupervised methods, admixture, and an in-depth treatment of multivariate methods, analysis of geographical structure with advice on how to handle GIS data together with genomic data, methods to assess past demographic events, and the analysis of natural selection, a traditional issue in evolutionary biology that has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).

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