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,
versions 3.X are not compatible with versions 2.0.X.
Note: optionally, vcf files can be imported using package vcfR. That package
is currently removed from CRAN, but can still be installed from
following instructions there.