Small example phased haplotype dataset and recombination map
Source:R/SmallHaps-data.R
SmallHaps.Rd
Simulated dataset with \(N=300\) haplotypes at \(L=400\) variants generated using msprime (Kelleher et al., 2016), together with the recombination map.
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
Kelleher, J., Etheridge, A. M., & McVean, G. (2016). Efficient coalescent simulation and genealogical analysis for large sample sizes. PLoS computational biology, 12(5).
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