Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
An S4 class containing furcation trees for one allele of a focal marke...
Convert a furcation tree into Newick format
Determine candidate regions of selection
EHH and iHH computation for a given focal marker
EHHS and iES computation for a given focal marker
calculate furcation trees around a focal marker
Calculate length of longest shared haplotypes around a focal marker
Calculate pairwise shared haplotype length between all chromosomes
Calculate score statistics for given regions
Calculate site frequency spectrum test statistics
Convert data from input file to an object of class haplohh
Plot distribution of standardized iHS, Rsb or XP-EHH values
Extract regions from a scan
Plot of unstandardized iHS within frequency bins
An S4 class to represent a furcation tree on one side of one allele of...
An S4 class representing the complete furcation pattern around a focal...
class for haplotype length
Class "haplohh"
Translate object of haplohh-class into SweepFinder format
Compute XP-EHH
Compute iHS
Compute Rsb
Copy example input files into current working directory
Manhattan plot of iHS, XP-EHH or Rsb over a genome.
Plot EHH around a focal marker
Plot EHHS around a focal marker
Plots furcation trees around a focal marker
Plot the length of extended haplotypes around a focal marker
Plot the variants of a haplohh object
rehh: Searching for Footprints of Selection using 'Extended Haplotype ...
Remove example files from current working directory.
Compute iHH, iES and inES over a whole chromosome without cut-offs
Compute iHH, iES and inES over a whole chromosome
Subsets object of haplohh-class
Update object of class haplohh
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) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
Useful links