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

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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.

Author
Mathieu Gautier and Renaud Vitalis
Date of publication
None
Maintainer
Mathieu Gautier <mathieu.gautier@supagro.inra.fr>
License
GPL(>=2)
Version
1.0

View on R-Forge

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...

Files in this package

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