sumstat_nSL: Number of Segregating Sites by Length

Description

This (mis)uses scan_hh from package rehh to calculate the nSL statistic from

Usage

sumstat_nSL(name = "ihh", position = NA, population = 1,
  max_snps = 10000)

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.

position

A position relative to the locus extent, e.g. 0.5 for the middle of the locus. If provided, the statistic will be calculate for the SNP closest to the given position. Otherwise, it will be calculated for all SNPs. The position is relative to the middle lo

population

The population for which the statistic is calculated.

max_snps

The maximal number of SNPs per locus that are used for the calculation. If a locus has more SNPs than this number, only a evenly distributed subset of this size will be used for calculating iHS to increase performance. Set to Inf to use all S

Value

When added to a model, the statistic returns a vector for each locus, which lists the values of nSL either for all SNPs when no position is given or for the SNP nearest to the selected position. SNPs are sorted by their positions on the locus.

Details

Ferrer-Admetlla et al., On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure. Mol Biol Evol (2014) 31 (5): 1275-1291. doi:10.1093/molbev/msu077

It uses the package rehh to calculate iHS with distances between SNPs measured in SNPs rather than in physical or genetic distance, which should result in nSL. It is required to install the package rehh to use this function.