# Searching for Footprints of Selection using Haplotype Homozygosity Based Tests

## Documentation for package ‘rehh’ version 2.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

rehh-package | Searching for footprints of selection using Haplotype Homozygosity based tests
bifurcation.diagram | plot of an haplotype bifurcation diagram
calc_ehh | EHH and iHH computations at a given core SNP
calc_ehhs | EHHS and iES computations at a given core SNP
data2haplohh | Converting data into an object of class haplohh
distribplot | Distribution of standardized iHS or Rsb values
haplohh-class | Class '"haplohh"'
haplohh_cgu_bta12 | Example of an 'haplohh' object
ies2rsb | Compute Rsb (standardized ratio of iES from two populations)
ies2xpehh | Compute xpEHH (standardized ratio of iES from two populations) as described in Sabeti et al. (2007)
ihh2ihs | Compute iHS (standardized iHH)
ihsplot | Plot iHS over a genome
make.example.files | Creating example input files
rehh | Searching for footprints of selection using Haplotype Homozygosity based tests
rsbplot | Plot Rsb over a genome
scan_hh | Computing EHH based statistics over a whole chromosome
xpehhplot | Plot XPEHH over a genome