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rehh (version 3.2.2)

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

Description

Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) , has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) and 'XP-EHH' (Sabeti 2007) , targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.

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Version

Install

install.packages('rehh')

Monthly Downloads

664

Version

3.2.2

License

GPL (>= 2)

Last Published

September 15th, 2021

Functions in rehh (3.2.2)

calc_candidate_regions

Determine candidate regions of selection
calc_region_stats

Calculate score statistics for given regions
as.newick

Convert a furcation tree into Newick format
calc_ehhs

EHHS and iES computation for a given focal marker
calc_haplen

Calculate length of longest shared haplotypes around a focal marker
allelefurcation-class

An S4 class containing furcation trees for one allele of a focal marker
calc_sfs_tests

Calculate site frequency spectrum test statistics
calc_ehh

EHH and iHH computation for a given focal marker
calc_furcation

calculate furcation trees around a focal marker
calc_pairwise_haplen

Calculate pairwise shared haplotype length between all chromosomes
ies2xpehh

Compute XP-EHH
freqbinplot

Plot of unstandardized iHS within frequency bins
scan_hh_full

Compute iHH, iES and inES over a whole chromosome without cut-offs
make.example.files

Copy example input files into current working directory
extract_regions

Extract regions from a scan
ines2rsb

Compute Rsb
scan_hh

Compute iHH, iES and inES over a whole chromosome
data2haplohh

Convert data from input file to an object of class haplohh
plot.haplen

Plot the length of extended haplotypes around a focal marker
plot.haplohh

Plot the variants of a haplohh object
distribplot

Plot distribution of standardized iHS, Rsb or XP-EHH values
subset.haplohh

haplohh-class

Class "haplohh"
haplen-class

class for haplotype length
ftree-class

An S4 class to represent a furcation tree on one side of one allele of a focal marker
furcation-class

An S4 class representing the complete furcation pattern around a focal marker.
haplohh2sweepfinder

Translate object of haplohh-class into SweepFinder format
ihh2ihs

Compute iHS
plot.ehh

Plot EHH around a focal marker
manhattanplot

Manhattan plot of iHS, XP-EHH or Rsb over a genome.
rehh-package

rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
remove.example.files

Remove example files from current working directory.
haplohh_cgu_bta12

Example of an haplohh object
update_haplohh

Update object of class haplohh
plot.ehhs

Plot EHHS around a focal marker
plot.furcation

Plots furcation trees around a focal marker