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.

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

View on CRAN

Files

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

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