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rehh (version 1.1)

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 (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

1.1

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

April 26th, 2013

Functions in rehh (1.1)

ihh2ihs

Compute iHS (standardized iHH)
calc_ehhs

EHHS and iES computations at a given core SNP
ies2rsb

Compute Rsb (standardized ratio of iES from two populations)
rsbplot

Plot Rsb over a genome
rehh-package

Searching for footprints of selection using Haplotype Homozygosity based tests
haplohh_cgu_bta12

Example of an haplohh object
scan_hh

Computing EHH based statistics over a whole chromosome
ihsplot

Plot iHS over a genome
distribplot

Distribution of standardized iHS or Rsb values
calc_ehh

EHH and iHH computations at a given core SNP
make.example.files

Creating example input files
bifurcation.diagram

plot of an haplotype bifurcation diagram
wgscan.cgu

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

Class "haplohh"
data2haplohh

Converting data into an object of class haplohh
wgscan.eut

Whole genome scan results for a pooled of European taurine cattle