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

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Documentation for package ‘rehh’ version 3.2.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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