Compute site-specific Extended Haplotype Homozygosity (EHHS) and integrated EHHS (iES) for a given focal SNP.
calc_ehhs(haplohh, mrk, limhaplo = 2, limehhs = 0.05,
scalegap = NA, maxgap = NA,
discard_integration_at_border = TRUE, plotehhs = TRUE,
lty = 1, lwd = 1.5, col = c("blue", "red"), xlab = "Position",
ylab = expression(Site ~ specific ~ italic(EHH) ~ (italic(EHHS))),
cex.lab = 1.25, main = NA, cex.main = 1.5)An object of class haplohh (see data2haplohh).
Either the number of the marker in the haplohh object (as integer) or its name (as string) to specify the focal marker
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
Limit at which EHHS stops to be evaluated
Scales gaps larger than the specified size to the specified size (default=NA, i.e. no scaling)
Maximum allowed gap in bp between two SNPs below which EHHS stops to be evaluated (default=NA, i.e., no limitation)
If TRUE and if first or last marker or a gap (larger than maxgap) is reached and EHHS is greater than limehh, then IES is set to NA
If TRUE, EHHS estimates are plotted for each position
Line type for the EHHS_Sabeti_et_al_2007 and EHHS_Tang_et_al_2007 (respectively) curves
Line width for the EHHS_Sabeti_et_al_2007 and EHHS_Tang_et_al_2007 (respectively) curves
Color for the EHHS_Sabeti_et_al_2007 and EHHS_Tang_et_al_2007 (respectively) curves
Legend for the x--axis
Legend for the y--axis
Size of the axis legend
Main legend of the EHHS plot
Size of the main legend
The returned value is a list containing the following elements:
A vector of nsnps columns containing EHHS estimates at each chromosome position relative to the focal SNP computed as described in the Tang et al. (2007).
A vector of nsnps columns containing EHHS estimates at each chromosome position relative to the focal SNP computed as described in the Sabeti et al. (2007).
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.
Integrated EHHS (computed using the estimator by Sabeti et al. (2007)) over the chromosome.
Integrated EHHS (computed using the estimator by Tang et al. (2007)) over the chromosome.
EHHS are computed at each position upstream and downstream of the focal SNP. This allows in turn the computation of the integrated EHHS relative to map distances (iES).
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. (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.
calc_ehh,data2haplohh,scan_hh
# NOT RUN {
#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)
# }
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