rehh: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests
Version 2.0.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorMathieu Gautier, Alexander Klassmann and Renaud Vitalis
Date of publication2016-11-18 12:43:14
MaintainerMathieu Gautier <mathieu.gautier@inra.fr>
LicenseGPL (>= 2)
Version2.0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rehh")

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)
ies2xpehh: Compute xpEHH (standardized ratio of iES from two...
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
xpehhplot: Plot XPEHH over a genome

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
ies2xpehh 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
xpehhplot Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/rehh.pdf
inst/doc/rehh.R
inst/doc/rehh.Rmd
src
src/Makevars
src/CALL_EHH.c
src/CALL_SCAN_HH.c
src/hh_utils.h
src/CALL_EHHS.c
src/hh_utils.c
NAMESPACE
data
data/haplohh_cgu_bta12.RData
data/datalist
R
R/calc_ehhs.R
R/rsbplot.R
R/xpehhplot.R
R/ies2xpehh.R
R/ihh2ihs.R
R/ihsplot.R
R/ies2rsb.R
R/scan_hh.R
R/calc_ehh.R
R/data2haplohh.R
R/distribplot.R
R/bifurcation.diagram.R
vignettes
vignettes/rehh.html
vignettes/genetics.csl
vignettes/rehh.Rmd
vignettes/vignette.bib
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/haplohh-class.Rd
man/calc_ehhs.Rd
man/ihsplot.Rd
man/data2haplohh.Rd
man/xpehhplot.Rd
man/ies2xpehh.Rd
man/distribplot.Rd
man/make.example.files.Rd
man/rsbplot.Rd
man/ihh2ihs.Rd
man/haplohh_cgu_bta12.Rd
man/rehh-package.Rd
man/bifurcation.diagram.Rd
man/calc_ehh.Rd
man/ies2rsb.Rd
man/scan_hh.Rd
rehh documentation built on May 20, 2017, 12:34 a.m.