scan_hh: Computing EHH based statistics over a whole chromosome

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

Description

Compute Extended Haplotype Homozygosity (EHH), site-specific EHH (EHHS), integrated EHH (iHH) and integrated EHHS (iES) for all SNPs of the chromosome (or linkage group).

Usage

scan_hh(haplohh,limhaplo=2,limehh=0.05,limehhs=0.05)

Arguments

haplohh	An object of class haplohh (see data2haplohh).
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
limehhs	Limit below which EHHS stops to be evaluated

Details

Extended Haplotype Homozygosity (EHH), site-specific EHH (EHHS), integrated EHH (iHH) and integrated EHHS (iES) are computed for all SNPs of the chromosome (or linkage group). This function is approximately twice as faster as a procedure calling in turn calc_ehh and calc_ehhs for all the SNP. To perform a whole genome-scan this function needs to be called for each chromosome and results concatenated.

Value

The returned value is a matrix with nsnps rows and six columns (Chromosome name, position of the SNP, Frequency of the ancestral allele, iHH for the ancestral allele, iHH for the derived allele and iES)

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.

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

calc_ehh,calc_ehhs,data2haplohh,ihh2ihs,ies2rsb

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12) 
res.scan<-scan_hh(haplohh_cgu_bta12)

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