sumstat_ihh: Integrated Extended Haplotype Homozygosity

Description

This summary statistic calculates a the iHH, iES and optionally iHS statistics.

Usage

sumstat_ihh(name = "ihh", population = 1, max_snps = 1000,
  calc_ihs = FALSE, 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.

max_snps

The maximal number of SNPs per locus that are used for the calculation. If a locus has more SNPs, only a random subset of them will be used to increase performance. Set to Inf to use all SNPs.

calc_ihs

If set to TRUE, additionally standardized iHS 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.

Value

When added to a model, the iHH statistics are calculated after simulation. If calc_ihs = FALSE, a data.frame with values for IHH and IES is returned. Otherwise, a list of two data.frame are returned, one for IHH and IES values and the other one for IHS values.
In all `data.frames` rows are SNPs and the colums present the following values for each SNP:
- CHR: The SNP's locus
Positions: The SNP's absolute position on its locus
FREQ_a: The SNP's absolute position on its locus
IHHa: integrated EHH for the ancestral allele
IHHd: integrated EHH for the derived allele
IES: integrated EHHS
iHS: iHS, normalized over all loci.

References

Mathieu Gautier and Renaud Vitalis, rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics (2012) 28 (8): 1176-1177 first published online March 7, 2012 doi:10.1093/bioinformatics/bts115

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

Details

Coala relies on scan_hh from package rehh to calculate this statistic. Please refer to their documentation for detailed information on the implementation. Please cite the corresponding publication (see below) if you use the statistic for a publication.