This function copies the following example files to the current working directory:
example1.hap "example 1" haplotype file in "standard format"
example1.map "example 1" marker information file
example1.vcf "example 1" as vcf file
example2.hap "example 2" haplotype file in "standard format"
example2.map "example 2" marker information file
example2.vcf "example 2" as vcf file
example_neutral.vcf "example neutral evolution" as vcf file
example_sweep.vcf "example for a selective sweep (without recombination)"
example_sweep_with_recombination.vcf "example for a selective sweep with recombination
ms.out output from a small simulation by the program 'ms'
bta12_cgu.hap an haplotype file in "standard format"
bta12_cgu.thap an haplotype file in "transposed format"
bta12_hapguess_switch.out an haplotype file in fastphase output format
map.inp a marker information file for all bta_cgu markers
Example 1 was used in (Gautier 2017) to explain the various EHH derived statistics calculated by this package. Example 2 is an extension containing multi-allelic markers and missing values.
Examples for neutral data and sweeps are discussed in a supplement of Klassmann (2020).
The bta12 files contain data for 280 haplotypes, originating from 140 individuals belonging to the Creole cattle breed from Guadeloupe, at 1.424 markers mapping to bovine chromosome 12 (BTA12) (Gautier 2011).
make.example.files()Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128-3143.
Gautier, M., Klassmann, A. and Vitalis, R. (2017). rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Molecular Ecology Resources, 17, 78-90.
Klassmann, A. and Gautier, M. (2020). Detecting selection using Extended Haplotype Homozygosity-based statistics on unphased or unpolarized data (preprint). https://doi.org/10.22541/au.160405572.29972398/v1