# Summary Statistic: Integrated Extended Haplotype Homozygosity

### Description

This summary statistic calculates a number of values based on
extended haplotype homozygosity (EHH), including iHH, iES
and optionally iHS.
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.

### Usage

1 2 | ```
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. Can also be "all" to calculate it from all populations. |

`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 |

`calc_ihs` |
If set to |

`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

If `calc_ihs = FALSE`

, a data.frame with values for
iHH and iES is returned. Otherwise, a list of two data frames 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.

### Author(s)

Paul Staab

### See Also

To create a demographic model: `coal_model`

To calculate this statistic from data: `calc_sumstats_from_data`

Other summary statistics: `sumstat_dna`

,
`sumstat_file`

,
`sumstat_four_gamete`

,
`sumstat_jsfs`

, `sumstat_mcmf`

,
`sumstat_nucleotide_div`

,
`sumstat_omega`

,
`sumstat_seg_sites`

,
`sumstat_sfs`

,
`sumstat_tajimas_d`

,
`sumstat_trees`

### Examples

1 2 3 4 5 6 7 | ```
model <- coal_model(20, 1, 1000) +
feat_mutation(1000) +
sumstat_ihh()
## Not run:
stat <- simulate(model)
print(stat$ihh)
## End(Not run)
``` |