sumstat_ihh: Integrated Extended Haplotype Homozygosity

Description

This summary statistic calculates a modified version of the iHH and iES statistics introduced by

Usage

sumstat_ihh(name = "ihh", position = NA, population = 1,
  max_snps = 1000)

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 matrix for each locus. The columns of the values state the values for integrated EHH for the ancestral allele (IHHa), integrated EHH for the derived allele (IHHd) and integrated EHHS (IES), either for all SNPs when no position is given or for the SNP nearest to the selected position. Each SNP is represented by a row, sorted by position on the locus.

Details

Voight et al., A map of recent positive selection in the human genome. PLoS Biol, 4(3):e72, Mar 2006

Coala relies on scan_hh from package rehh to calculate this statistic. Please refer to their documentation for detailed information on the implementation.