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rehh (version 1.12)

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

866

Version

1.12

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

April 7th, 2015

Functions in rehh (1.12)

distribplot

Distribution of standardized iHS or Rsb values
calc_ehh

EHH and iHH computations at a given core SNP
ihh2ihs

Compute iHS (standardized iHH)
scan_hh

Computing EHH based statistics over a whole chromosome
rehh-package

Searching for footprints of selection using Haplotype Homozygosity based tests
make.example.files

Creating example input files
wgscan.cgu

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

Plot Rsb over a genome
ies2rsb

Compute Rsb (standardized ratio of iES from two populations)
wgscan.eut

Whole genome scan results for a pooled of European taurine cattle
haplohh-class

Class "haplohh"
data2haplohh

Converting data into an object of class haplohh
haplohh_cgu_bta12

Example of an haplohh object
calc_ehhs

EHHS and iES computations at a given core SNP
ihsplot

Plot iHS over a genome
bifurcation.diagram

plot of an haplotype bifurcation diagram