Small example phased haplotype dataset and recombination map

Simulated dataset with \(N=300\) haplotypes at \(L=400\) variants generated using msprime (Kelleher et al., 2016), together with the recombination map.

Usage

data("SmallHaps")

data("SmallMap")

Format

For SmallHaps, an object of class matrix of dimensions \(400 \times 300\) where each column is a simulated haplotype. This is suitable for passing directly to CacheHaplotypes().

For SmallMap, a vector of length 400 representing the recombination map for the SmallHaps data. This can be used with CalcRho(), by converting to recombination distances using diff(SmallMap).

References

Aslett, L.J.M. and Christ, R.R. (2024) "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R", BMC Bioinformatics, 25(1). Available at: doi:10.1186/s12859-024-05688-8 .

Kelleher, J., Etheridge, A.M. and McVean, G. (2016) "Efficient coalescent simulation and genealogical analysis for large sample sizes", PLoS Computational Biology, 12(5). Available at: doi:10.1371/journal.pcbi.1004842 .

Examples

data("SmallHaps")

# \donttest{
# Plot Allele Frequencies
hist(rowMeans(SmallHaps),breaks=20)

# }

# Import into kalis cache directly ...
CacheHaplotypes(SmallHaps)
#> Warning: haplotypes already cached ... overwriting existing cache.

data("SmallMap")

# Find parameters
pars <- Parameters(CalcRho(diff(SmallMap)))
pars
#> Parameters object with:
#>   rho   = (0.030722976221863, 0.00188322071638501, 6.79809190046651e-06, ..., 1.56898508137998e-05, 1.7924679243824e-05, 1)
#>   mu    = 1e-08
#>   Pi    = 0.00334448160535117