Linking genomics and population genetics with R. (29th August 2016)

• Record Type: Journal Article
• Authors: Paradis, Emmanuel; Gosselin, Thierry; Goudet, Jérôme; Jombart, Thibaut; Schliep, Klaus
• Is Part Of: Molecular ecology resources. Volume 17:Number 1(2017:Jan.)
• Page Start: 54
• Page End: 66
• Publication Date: 2016-08-29
• Subjects: multivariate analysis -- next‐generation sequencing -- r -- single‐nucleotide polymorphism -- variant call format; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12577
• Languages: English
• ISSNs: 1755-098X

Abstract

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 howr, 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 ofr software for population genomics.