rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

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) <doi: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) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics. Due to changes in the API, albeit mostly minor, this version is not compatible with versions 2.0.X.

Version: 3.0.1
Depends: R (≥ 2.10)
Imports: methods, rehh.data
Suggests: ape, bookdown, gap, knitr, qqman, rmarkdown, testthat, vcfR
Published: 2019-07-11
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh at oneoverx.eu>
BugReports: https://gitlab.com/oneoverx/rehh/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://CRAN.R-project.org/package=rehh, https://gitlab.com/oneoverx/rehh
NeedsCompilation: yes
Citation: rehh citation info
Materials: NEWS
CRAN checks: rehh results

Downloads:

Reference manual: rehh.pdf
Vignettes: Examples in detail
How to use rehh
Package source: rehh_3.0.1.tar.gz
Windows binaries: r-devel: rehh_3.0.1.zip, r-release: rehh_3.0.1.zip, r-oldrel: rehh_3.0.1.zip
OS X binaries: r-release: rehh_3.0.1.tgz, r-oldrel: rehh_3.0.1.tgz
Old sources: rehh archive

Reverse dependencies:

Reverse imports: coala

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