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

Population genetic data in form of "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. The concept of an "Extended Haplotype Homozygosity" (EHH), introduced by (Sabeti 2002) , has given rise to several derived statistics designed for whole genome scans. The package provides functions to compute three of these, namely: "iHS" (Voight 2006) for detecting selection within a single population as well as "Rsb" (Tang 2007) and "XP-EHH" (Sabeti 2007) to detect (differential) selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics.


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2.0.4 by Mathieu Gautier, 4 days ago

Browse source code at

Authors: Mathieu Gautier , Alexander Klassmann and Renaud Vitalis

Documentation:   PDF Manual  

GPL (>= 2) license

Depends on, gplots, methods

Suggests knitr, rmarkdown, bookdown

Imported by coala.

See at CRAN