title: Linking genomics and population genetics with R.
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 single-nucleotide polymorphism data, handling and reading variant call format 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.
authors.affiliation: Institut des Sciences de l'Évolution, Université Montpellier - CNRS - IRD - EPHE, Place Eugène Bataillon - CC 065, 34095, Montpellier cédex 05, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Paradis
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Thierry
authors.initials: T
authors.lastname: Gosselin
authors.affiliation: Department of Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Goudet
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, W2 1PG, UK.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Jombart
authors.affiliation: Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schliep
mesh_terms: D056808:Biostatistics / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software
keywords: 
  r
  ; multivariate analysis; next-generation sequencing; single-nucleotide polymorphism; variant call format