EHH decay curves for the ancestral (0) and derived (1) core-allele
carriers (Ehhdec), each integrated by the trapezoid
rule outward from the core until EHH < min_ehh (0.05 in the
paper), giving iHH_A and iHH_D; unstandardized iHS =
ln(iHH_A / iHH_D) (Voight et al. 2006, eq. 1). Pass
standardize = c(mean, sd) of a genome-wide reference for the
frequency-bin z-score of their eq. 2.
Usage
Ihstst(hap, core, positions = NULL, min_ehh = 0.05, standardize = NULL)
Arguments
- hap
Phased 0/1 haplotype matrix (chromosomes x SNPs);
1 = derived.
- core
Core SNP index (1-based).
- positions
Optional positions; index scale by default.
- min_ehh
Integration threshold (default 0.05).
- standardize
Optional c(mean, sd) for the z-score.
Value
List with estimate, ihs_unstandardized,
ihh_a, ihh_d, daf, truncated_a,
truncated_d, standardized, core,
method.
References
Voight, B. F., Kudaravalli, S., Wen, X. and Pritchard,
J. K. (2006), PLoS Biology 4(3), e72, eqs. (1)-(2) and Materials
and Methods "Calculation of iHS". Sabeti, P. C. et al. (2002),
Nature 419, 832-837.
Examples
set.seed(1)
hap <- matrix(rbinom(40 * 21, 1, 0.4), 40, 21)
hap[, 11] <- rep(c(0, 1), each = 20)
r <- Ihstst(hap, core = 11, positions = 1:21)
is.list(r)
#> [1] TRUE
