Linking genomics and population genetics with R
File(s)
Accepted version
Author(s)
Paradis, E
Gosselin, T
Goudet, J
Jombart, T
Schliep, K
Type
Journal Article
Abstract
Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re-)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collected on many individuals. We then expose how R, as a computing language and development environment, proposes some solutions to meet these challenges. We focus on some specific issues that are often encountered in practice: handling and analysing SNP data, handling and reading VCF files, analysing haplotypes and linkage disequilibrium, and performing multivariate analyses. We illustrate these implementations with some analyses of three recently published data sets that contain between 60,000 and 1,000,000 loci. We conclude with some perspectives on future developments of R software for population genomics. This article is protected by copyright. All rights reserved.
Date Issued
2016-08-29
Date Acceptance
2016-07-23
Citation
Molecular Ecology Resources, 2016, 17 (1), pp.54-66
ISSN
1755-0998
Publisher
Wiley
Start Page
54
End Page
66
Journal / Book Title
Molecular Ecology Resources
Volume
17
Issue
1
Copyright Statement
© 2016 John Wiley & Sons Ltd. This is the peer reviewed version of the following article: Paradis, E., Gosselin, T., Goudet, J., Jombart, T. and Schliep, K. (2016), Linking genomics and population genetics with R. Mol Ecol Resour. , which has been published in final form at https://dx.doi.org/10.1111/1755-0998.12577. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.
Sponsor
Medical Research Council (MRC)
Grant Number
MR/K010174/1B
Subjects
NGS
SNP
VCF
R
multivariate analysis
Publication Status
Published