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.
sumstat_ihh(
name = "ihh",
population = 1,
max_snps = 1000,
calc_ihs = FALSE,
transformation = identity
)
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 columns present the following
values for each SNP:
CHR: The SNP's locus
POSITION: The SNP's absolute position on its locus
FREQ_A: The frequency of the ancestral allele
FREQ_D: The frequency of the derived allele
IHH_A: integrated EHH for the ancestral allele
IHH_D: integrated EHH for the derived allele
IES: integrated EHHS
INES: integrated normalized EHHS
IHS: iHS, normalized over all loci.
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.
The population for which the statistic is calculated. Can also be "all" to calculate it from all populations. Default is population 1.
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.
If set to TRUE
, additionally standardized iHS is
calculated.
An optional function for transforming the results of the statistic. If specified, the results of the transformation are returned instead of the original values.
Paul Staab
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.
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()
model <- coal_model(20, 1, 1000) +
feat_mutation(1000) +
sumstat_ihh()
# \donttest{
stat <- simulate(model)
print(stat$ihh)# }
Run the code above in your browser using DataLab