CRAN/E | rehh

rehh

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

Installation

About

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 included to facilitate visualization and interpretation of these statistics.

Citation rehh citation info
CRAN.R-project.org/package=rehh
gitlab.com/oneoverx/rehh
Bug report File report

Key Metrics

Version 3.2.2
R ≥ 2.10
Published 2021-09-15 1118 days ago
Needs compilation? yes
License GPL-2
License GPL-3
CRAN checks rehh results

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Maintainer

Maintainer

Alexander Klassmann

Authors

Alexander Klassmann

aut / cre

Mathieu Gautier

aut

Renaud Vitalis

aut

Material

NEWS
Reference manual
Package source

Vignettes

Examples in detail
Vignette for package *rehh*

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

rehh archive

Depends

R ≥ 2.10

Imports

methods
rehh.data

Suggests

ape
bookdown
data.table
gap
knitr
qqman
rmarkdown
R.utils
testthat
vcfR

Reverse Imports

coala