Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests

Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb or XP-EHH (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.

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) <doi:10.1038/nature01140>, 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) <doi:10.1371/journal.pbio.0040072> for
detecting 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> to detect
(differential) selection between two populations.
Various plotting functions are also included to facilitate
visualization and interpretation of these statistics.

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