calc_ehhs: EHHS and iES computations at a given core SNP

In theboocock/rehh: Searching for footprints of selection using Haplotype Homozygosity based tests

Description

Compute site Extended Haplotype Homozygosity (EHHS) and integrated EHH (iES) for a given focal SNPs.

Usage

calc_ehhs(haplohh,mrk,limhaplo=2,limehhs=0.05,
plotehhs=TRUE,main_leg="EHHS plot")

Arguments

haplohh	An object of class haplohh (see data2haplohh).
mrk	Integer representing the number of the focal marker
limhaplo	Minimal number of haplotypes to continue computing EHHS away from the core SNP. Useless, if no missing data. However, when some data are missing, haplotypes with missing data are removed from the computation. Hence as we compute EHH further from the core SNP, less haplotypes are expected
limehhs	Limit below which EHHS stops to be evaluated
plotehhs	If TRUE, EHHS estimates are plotted for each position
main_leg	Legend of the EHHS plot

Details

EHHS are computed at each position upstream and downstream the focal SNP. This allows in turn the computation of the integrated EHHS relative to map distances (iES).

Value

The returned value is a list containing the following components:

ehhs	A vector of nsnps columns containing EHHS estimates at each chromosome position relative to the focal SNP.
nhaplo_eval	A matrix of two rows and nsnps columns containing the number of evaluated haplotypes at each chromosome position relative to the focal SNP for the ancestral (first row) and derived (second row) alleles.
freqall1	Frequency of the ancestral allele matrix for the focal SNP.
ies	Integrated EHHS (IES) over the chromosome.

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.

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.

See Also

calc_ehh,data2haplohh,scan_hh

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12) 
#computing EHH statistics for the focal SNP at position 456
#which displays a strong signal of selection
res.ehhs<-calc_ehhs(haplohh_cgu_bta12,mrk=456)

theboocock/rehh documentation built on May 31, 2019, 9:11 a.m.