calc_ehhs {rehh}

EHHS and iES computation for a given focal marker

Description

Compute site-specific Extended Haplotype Homozygosity (EHHS) and integrated EHHS (iES) for a given focal marker.

Usage

calc_ehhs(
  haplohh,
  mrk,
  limhaplo = 2,
  limhomohaplo = 2,
  limehhs = 0.05,
  include_zero_values = FALSE,
  include_nhaplo = FALSE,
  phased = TRUE,
  scalegap = NA,
  maxgap = NA,
  discard_integration_at_border = TRUE,
  lower_y_bound = limehhs,
  interpolate = TRUE
)

Arguments

haplohh

an object of class haplohh (see data2haplohh).

mrk

integer representing the number of the focal marker within the haplohh object or string representing its ID/name.

limhaplo

if there are less than limhaplo chromosomes that can be used for the calculation of EHH, the calculation is stopped. The option is intended for the case of missing data, which leads to the successive exclusion of haplotypes: the further away from the focal marker the less haplotypes contribute to EHH.

limhomohaplo

if there are less than limhomohaplo homozygous chromosomes, the calculation is stopped. This option is intended for unphased data and should be invoked only if relatively low frequency variants are not filtered subsequently (see main vignette and Klassmann et al. 2020).

limehhs

limit at which EHHS stops to be evaluated.

include_zero_values

logical. If FALSE, return values only for those positions where the calculation is actually performed, i.e. until stopped by reaching either limehh or limhaplo. If TRUE, report EHH values for all markers, the additional ones being zero.

include_nhaplo

logical. If TRUE, report the number of evaluated haplotypes at each marker (only informative, if missing data leads to a decrease of evaluated haplotypes).

phased

logical. If TRUE (default) chromosomes are expected to be phased. If FALSE, the haplotype data is assumed to consist of pairwise ordered chromosomes belonging to diploid individuals. EHHS is then estimated over individuals which are homozygous at the focal marker.

scalegap

scale or cap gaps larger than the specified size to the specified size (default=NA, i.e. no scaling).

maxgap

maximum allowed gap in bp between two markers. If exceeded, further calculation of EHHS is stopped at the gap (default=NA, i.e no limitation).

discard_integration_at_border

logical. If TRUE (default) and computation reaches first or last marker or a gap larger than maxgap, iHH is set to NA.

lower_y_bound

lower y boundary of the area to be integrated over (default: limehhs). Can be set to zero for compatibility with the program hapbin.

interpolate

logical. Affects only IES and INES values. If TRUE (default), integration is performed over a continuous EHHS curve (values are interpolated linearly between consecutive markers), otherwise the EHHS curve decreases stepwise at markers.

Details

Values for site-specific Extended Haplotype Homozygosity (EHHS) are computed at each position upstream and downstream of the focal marker. These values are integrated with respect to their genomic position to yield an 'integrated EHHS' (iES) value.

Value

The returned value is a list containing the following elements:

mrk.name

The name/identifier of the focal marker.

ehhs

A table containing EHHS values as used by Sabeti et al. (2007), resp. the same values normalized to 1 at the focal marker (nEHHS) as used by Tang et al. (2007).

IES

Integrated EHHS.

INES

Integrated normalized EHHS.

References

Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128-3143.

Klassmann, A. and Gautier, M. (2020). Detecting selection using Extended Haplotype Homozygosity-based statistics on unphased or unpolarized data (preprint). https://doi.org/10.22541/au.160405572.29972398/v1

Sabeti, P.C. et al. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.

Sabeti, P.C. et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449, 913-918.

Tang, K. and Thornton, K.R. and Stoneking, M. (2007). A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. Plos Biology, 7, e171.

Voight, B.F. and Kudaravalli, S. and Wen, X. and Pritchard, J.K. (2006). A map of recent positive selection in the human genome. Plos Biology, 4, e72.

See Also

data2haplohh, plot.ehhs, calc_ehh, scan_hh.

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#computing EHHS statistics for the marker "F1205400"
#which displays a strong signal of selection
ehhs <- calc_ehhs(haplohh_cgu_bta12, mrk = "F1205400")