rehh (version 1.1)

rehh-package: Searching for footprints of selection using Haplotype Homozygosity based tests

Description

Functions for the detection of footprints of selection on dense SNP data using Extended Homozygosity Haplotype (EHH) based tests. The package includes computation of EHH, iHS (within population) and Rsb (across pairs of populations) statistics. Various plotting functions are also included to facilitate visualization and interpretation of the results.

Details

ll{ Package: rehh Version: 1.1 License: GPL(>=2) Depends: gplots , methods }

Index: 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_cgu_bta12 Example of an 'haplohh' object ies2rsb Compute Rsb (standardized ratio of iES from two populations) ihh2ihs Compute iHS (standardized iHH) ihsplot Plot iHS over a genome make.example.files Generate example input files rsbplot Plot Rsb over a genome scan_hh Computing EHH based statistics over a whole chromosome wgscan.cgu Whole genome scan results for the CGU (Creole from Guadeloupe island) wgscan.eut Whole genome scan results for a pool of European taurine cattle

References

Gautier, M. and Vitalis, R. (2012). rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, 28(8), 1176--1177.