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rehh (version 2.0.1)

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 or XP-EHH (across pairs of populations) statistics. Various plotting functions are also included to facilitate visualization and interpretation of the results.

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Version

Install

install.packages('rehh')

Monthly Downloads

523

Version

2.0.1

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

October 25th, 2016

Functions in rehh (2.0.1)

Plot XPEHH over a genome

haplohh_cgu_bta12

Example of an haplohh object

EHH and iHH computations at a given core SNP

bifurcation.diagram

plot of an haplotype bifurcation diagram

EHHS and iES computations at a given core SNP

Compute iHS (standardized iHH)

Distribution of standardized iHS or Rsb values

Converting data into an object of class haplohh

Compute xpEHH (standardized ratio of iES from two populations) as described in Sabeti et al. (2007)

Compute Rsb (standardized ratio of iES from two populations)

Class "haplohh"

Plot iHS over a genome

Searching for footprints of selection using Haplotype Homozygosity based tests

Whole genome scan results for a pool of European taurine cattle

make.example.files

Creating example input files

Whole genome scan results for the CGU (Creole from Guadeloupe island)

Computing EHH based statistics over a whole chromosome

Plot Rsb over a genome