sumstat_four_gamete: A Summary Statistic based on the Four-Gamete-Condition
Description
The Four-Gamete-Condition for two SNPs is violated if all four combinations
of derived and ancestral alleles at the SNPs are observed in a gamete/a
haplotype. Under an Infinite-Sites mutation model, a violation indicates that
there must have been at least one recombination event between the SNPs.
This summary statistic calculates the percentage of certain pairs of SNPs
that violate the Four-Gamete-Condition.
It is sensitive for recombination and particularly useful when estimating
recombination rates.
Usage
sumstat_four_gamete(name = "four_gamete", population = 1,
transformation = identity)
Arguments
name
The name of the summary statistic. When simulating a model,
the value of the statistics are written to an entry of the returned list
with this name. Summary statistic names must be unique in a model.
population
The population for which the statistic is calculated.
transformation
An optional function for transforming the results
of the statistic. If specified, the results of the transformation are
returned instead of the original values.
Details
The statistic generates a matrix where each row represents one locus, and the
columns give the statistic for different classes of pairs of SNPs: