Population genetic data such as ‘Single Nucleotide Polymorphisms’ (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an ‘Extended Haplotype Homozygosity’ (EHH), introduced by Sabeti (2002) (https://doi.org/10.1038/nature01140), has given rise to several statistics designed for whole genome scans.
The package provides functions to compute three of these, namely: ‘iHS’ (Voight 2006) (https://doi.org/10.1371/journal.pbio.0040072) for detecting positive or ‘Darwinian’ selection within a single population as well as ‘Rsb’ (Tang 2007) (https://doi.org/10.1371/journal.pbio.0050171) and ‘XP-EHH’ (Sabeti 2007) (https://doi.org/10.1038/nature06250), targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
Alexander Klassmann, Mathieu Gautier & Renaud Vitalis
Gautier M & Vitalis R, 2012. rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, 28(8), 1176-1177. (https://doi.org/10.1093/bioinformatics/bts115)
Gautier M, Klassmann A & Vitalis R, 2017. REHH 2.0: a reimplementation of the R package REHH to detect positive selection from haplotype structure. Molecular Ecology Resources, 17(1), 78-90. (https://doi.org/10.1111/1755-0998.12634).
By A. Klassmann on 2022-10-14
