make.example.files

This function copies the following example files to the working directory:<ul>
<li><code>bta12_cgu.hap</code> an haplotype input file in standard format</li>
<li><code>bta12_cgu.thap</code> an haplotype input file in transposed format</li>
<li><code>bta12_hapguess_switch.out</code> an haplotype input file in fastphase output format</li>
<li><code>map.inp</code> a SNP information input file</li>
</ul>These files contain data for 280 haplotypes (originating from 140 individuals belonging to the Creole
cattle breed from Guadeloupe) of 1,424 SNPs mapping to bovine chromosome 12 (BTA12) (see reference below).

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.

Mathieu Gautier

make.example.files: Creating example input files

Description

Usage

Arguments

References

See Also

Examples