rehh: Searching for footprints of selection using Haplotype Homozygosity based tests
Version 1.0

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 facilate vizualisation and interpretation of the results.

AuthorMathieu Gautier and Renaud Vitalis
Date of publicationNone
MaintainerMathieu Gautier <mathieu.gautier@supagro.inra.fr>
LicenseGPL(>=2)
Version1.0
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rehh", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

bifurcation.diagram: plot of an haplotype bifurcation diagram
calc_ehhs: EHHS and iES computations at a given core SNP
haplohh-class: Class '"haplohh"'
ihsplot: Plot iHS over a genome
make.example.files: Creating example input files
rehh-package: Searching for footprints of selection using Haplotype...
rsbplot: Plot Rsb over a genome
See all...

All man pages Function index File listing

Man pages

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
haplohh-class: Class '"haplohh"'
ies2rsb: Compute Rsb (standardized ratio of iES from two populations)
ihh2ihs: Compute iHS (standardized iHH)
ihsplot: Plot iHS over a genome
make.example.files: Creating example input files
rehh-package: Searching for footprints of selection using Haplotype...
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...
wgscan.eut: Whole genome scan results for a pooled of European taurine...

Functions

bifurcation.diagram Man page Source code
calc_ehh Man page Source code
calc_ehhs Man page Source code
data2haplohh Man page Source code
distribplot Man page Source code
haplohh-class Man page
haplohh_cgu_bta12 Man page
ies2rsb Man page Source code
ihh2ihs Man page Source code
ihsplot Man page Source code
is.haplohh Source code
make.example.files Man page Source code
rehh Man page
rehh-package Man page
rsbplot Man page Source code
scan_hh Man page Source code
wgscan.cgu Man page
wgscan.eut Man page

Files

data
data/datalist
data/haplohh_cgu_bta12.RData
data/wgscan.cgu.RData
data/wgscan.eut.RData
R
R/bifurcation.diagram.R
R/calc_ehhs.R
R/data2haplohh.R
R/rsbplot.R
R/calc_ehh.R
R/ihh2ihs.R
R/ihsplot.R
R/ies2rsb.R
R/scan_hh.R
R/distribplot.R
NAMESPACE
inst
inst/bta12_hapguess_switch.out
inst/CITATION
inst/map.inp
inst/bta12_cgu.hap
DESCRIPTION
man
man/wgscan.cgu.Rd
man/rehh-package.Rd
man/scan_hh.Rd
man/haplohh-class.Rd
man/wgscan.eut.Rd
man/calc_ehhs.Rd
man/calc_ehh.Rd
man/data2haplohh.Rd
man/rsbplot.Rd
man/ihsplot.Rd
man/make.example.files.Rd
man/distribplot.Rd
man/bifurcation.diagram.Rd
man/ies2rsb.Rd
man/ihh2ihs.Rd
man/haplohh_cgu_bta12.Rd
src
src/ehh_utils.c
src/r_ehhs.c
src/r_scan_hh.c
src/r_ehh.c
src/ehh_utils.h
rehh documentation built on May 21, 2017, 1:09 a.m.

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