scan_hh: Computing EHH based statistics over a whole chromosome

Description Usage Arguments Details Value References See Also Examples

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

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scan_hh(haplohh,limhaplo=2,limehh=0.05,limehhs=0.05,maxgap=NA,threads=1)

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

maxgap

Maximum allowed gap in bp between two SNPs below which EHH and EHHS stop to be evaluated (default=NA, i.e., no limitation)

threads

Number of threads to parallelize compuation

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 several times 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 dataframe with nsnps rows and seven columns (Chromosome name, position of the SNP, Frequency of the ancestral allele, iHH for the ancestral allele, iHH for the derived allele, iES using the estimator by Sabeti et al. (2007) estimator and iES using the estimator by Tang et al. (2007))

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. 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

calc_ehh,calc_ehhs,data2haplohh,ihh2ihs,ies2rsb

Examples

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


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