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.

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Description file content

Package
rehh
Maintainer
Alexander Klassmann
Author
Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Version
3.0.1
License
GPL (>= 2)
Title
Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
Description
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) , has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) and 'XP-EHH' (Sabeti 2007) , 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.
Depends
R (>= 2.10)
Imports
methods, rehh.data
Suggests
ape, bookdown, gap, knitr, qqman, rmarkdown, testthat, vcfR
VignetteBuilder
knitr
NeedsCompilation
yes
Packaged
2019-07-11 09:28:26 UTC; alex
RoxygenNote
6.1.1
URL
BugReports
https://gitlab.com/oneoverx/rehh/issues
Repository
CRAN
Date/Publication
2019-07-11 13:42:50 UTC

install.packages('rehh')

3.0.1

7 days ago

https://CRAN.R-project.org/package=rehh

Alexander Klassmann

GPL (>= 2)

Depends on

R (>= 2.10)

Imports

methods, rehh.data

Suggests

ape, bookdown, gap, knitr, qqman, rmarkdown, testthat, vcfR

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