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

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.

Author
Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Date of publication
2016-11-18 12:43:14
Maintainer
Mathieu Gautier <mathieu.gautier@inra.fr>
License
GPL (>= 2)
Version
2.0.2

View on CRAN

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

Files in this package

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