allelefurcation-class

allelefurcation

An S4 class containing the furcation trees
for both sides of a focal marker for one allele.

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.

Alexander Klassmann

rehh

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

Mathieu Gautier

Renaud Vitalis

allelefurcation-class function

<dl class="dl-horizontal">
<dt><code>allele</code></dt><dd>the allele of the focal marker.</dd></dl><dt><code>description</code></dt><dd>"ancestral", "derived", "major", "minor", etc.</dd><dt><code>count</code></dt><dd>the number of chromosomes with that allele.</dd><dt><code>left</code></dt><dd>furcation tree to the left of the marker.</dd><dt><code>right</code></dt><dd>furcation tree to the right of the marker.</dd>

allelefurcation-class: An S4 class containing furcation trees for one allele of a focal marker

Description

Arguments

Slots

See Also