# Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

## Documentation for package ‘rehh’ version 3.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

rehh-package | rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
allelefurcation | An S4 class containing furcation trees for one allele of a focal marker
allelefurcation-class | An S4 class containing furcation trees for one allele of a focal marker
as.newick | Convert a furcation tree into Newick format
calc_candidate_regions | Determine candidate regions of selection
calc_ehh | EHH and iHH computation for a given focal marker
calc_ehhs | EHHS and iES computation for a given focal marker
calc_furcation | calculate furcation trees around a focal marker
calc_haplen | Calculate length of longest shared haplotypes around a focal marker
calc_pairwise_haplen | Calculate pairwise shared haplotype length between all chromosomes
calc_region_stats | Calculate score statistics for given regions
calc_sfs_tests | Calculate site frequency spectrum test statistics
chr.name | Class "haplohh"
chr.name, | Class "haplohh"
chr.name-method | Class "haplohh"
data2haplohh | Convert data from input file to an object of class haplohh
distribplot | Plot distribution of standardized iHS, Rsb or XP-EHH values
ehh | EHH and iHH computation for a given focal marker
ehh-class | EHH and iHH computation for a given focal marker
ehhs | EHHS and iES computation for a given focal marker
ehhs-class | EHHS and iES computation for a given focal marker
extract_regions | Extract regions from a scan
freqbinplot | Plot of unstandardized iHS within frequency bins
ftree | An S4 class to represent a furcation tree on one side of one allele of a focal marker
ftree-class | An S4 class to represent a furcation tree on one side of one allele of a focal marker
furcation | An S4 class representing the complete furcation pattern around a focal marker.
furcation-class | An S4 class representing the complete furcation pattern around a focal marker.
hap.names | Class "haplohh"
hap.names, | Class "haplohh"
hap.names-method | Class "haplohh"
haplen | class for haplotype length
haplen-class | class for haplotype length
haplo | Class "haplohh"
haplo, | Class "haplohh"
haplo-method | Class "haplohh"
haplohh-class | Class "haplohh"
haplohh2sweepfinder | Translate object of 'haplohh-class' into SweepFinder format
haplohh_cgu_bta12 | Example of an 'haplohh' object
ies2xpehh | Compute XP-EHH
ihh2ihs | Compute iHS
ines2rsb | Compute Rsb
make.example.files | Copy example input files into current working directory
manhattanplot | Manhattan plot of iHS, XP-EHH or Rsb over a genome.
mrk.names | Class "haplohh"
mrk.names, | Class "haplohh"
mrk.names-method | Class "haplohh"
nhap | Class "haplohh"
nhap, | Class "haplohh"
nhap-method | Class "haplohh"
nmrk | Class "haplohh"
nmrk, | Class "haplohh"
nmrk-method | Class "haplohh"
plot.ehh | Plot EHH around a focal marker
plot.ehhs | Plot EHHS around a focal marker
plot.furcation | Plots furcation trees around a focal marker
plot.haplen | Plot the length of extended haplotypes around a focal marker
plot.haplohh | Plot the variants of a haplohh object
positions | Class "haplohh"
positions, | Class "haplohh"
positions-method | Class "haplohh"
rehh | rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
remove.example.files | Remove example files from current working directory.
scan_hh | Compute iHH, iES and inES over a whole chromosome
scan_hh_full | Compute iHH, iES and inES over a whole chromosome without cut-offs
subset.haplohh | Subsets object of 'haplohh-class'
update_haplohh | Update object of class haplohh