calc_ehh: EHH and iHH computations at a given core SNP

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

Description

Compute Extended Haplotype Homozygosity (EHH) and integrated EHH (iHH) for a given focal SNPs.

Usage

calc_ehh(haplohh,mrk,limhaplo=2,limehh=0.05,
plotehh=TRUE,main_leg="EHH 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 EHH 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
limehh	Limit below which EHH stops to be evaluated
plotehh	If TRUE, EHH estimates for both the ancestral and derived allele are plotted for each position
main_leg	Legend of the EHH plot.

Details

EHH are computed at each position upstream and downstream the focal SNP for both the derived and ancestral allele. This allows in turn the computation of the integrated EHH relative to map distances (iHH).

Value

The returned value is a list containing the following components:

ehh	A matrix of two rows and nsnps columns containing EHH estimates at each chromosome position relative to the focal SNP for the ancestral (first row) and derived (second row) alleles.
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.
ihh	A vector of two elements corresponding respectively to the iHH (integrated EHH) for the ancestral and derived allele.

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.

Sabeti, P.C. and Reich, D.E. and Higgins, J.M. and Levine, H.Z.P and Richter, D.J. and Schaffner, S.F. and Gabriel, S.B. and Platko, J.V. and Patterson, N.J. and McDonald, G.J. and Ackerman, H.C. and Campbell, S.J. and Altshuler, D. and Cooper, R. and Kwiatkowski, D. and Ward, R. and Lander, E.S. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832–837.

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

calc_ehhs,data2haplohh,scan_hh

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12) 

#computing EHH statisitics for the focal SNP at position 456
# which displays a strong signal of selection
res.ehh<-calc_ehh(haplohh_cgu_bta12,mrk=456)

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