calc_region_stats

a data frame containing scores (output of <code><a rd-options="" href="/link/ihh2ihs?package=rehh&version=3.2.2" data-mini-rdoc="rehh::ihh2ihs">ihh2ihs</a></code>, <code><a rd-options="" href="/link/ines2rsb?package=rehh&version=3.2.2" data-mini-rdoc="rehh::ines2rsb">ines2rsb</a></code> or <code><a rd-options="" href="/link/ies2xpehh?package=rehh&version=3.2.2" data-mini-rdoc="rehh::ies2xpehh">ies2xpehh</a></code>).

scan

a data frame with column names <code>CHR</code>, <code>START</code> and <code>END</code>,
specifying chromosomal regions (e.g. as obtained by function <code><a rd-options="" href="/link/calc_candidate_regions?package=rehh&version=3.2.2" data-mini-rdoc="rehh::calc_candidate_regions">calc_candidate_regions</a></code>).

regions

boundary score above which markers are defined as "extreme".

threshold

logical. If <code>TRUE</code> use the (negative log-) p-value instead of the score.

pval

logical. If <code>TRUE</code> (default), take absolute values of score.

ignore_sign

logical, indicating if the regions should be closed on the right (and open on the left) or vice versa.

right

Calculate score statistics (extremal values) for given regions. This function
is intended for the comparison of different scores for the same chromosomal regions.

Population genetic data such as 'Single Nucleotide
Polymorphisms' (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH),
introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
at differential selection between two populations.
Various plotting functions are included to facilitate
visualization and interpretation of these statistics.

Alexander Klassmann

rehh

Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests

Mathieu Gautier

Renaud Vitalis

calc_region_stats function

a data frame containing scores (output of <code><a rd-options='' href='ihh2ihs'>ihh2ihs</a></code>, <code><a rd-options='' href='ines2rsb'>ines2rsb</a></code> or <code><a rd-options='' href='ies2xpehh'>ies2xpehh</a></code>).

a data frame with column names <code>CHR</code>, <code>START</code> and <code>END</code>,
specifying chromosomal regions (e.g. as obtained by function <code><a rd-options='' href='calc_candidate_regions'>calc_candidate_regions</a></code>).

calc_region_stats: Calculate score statistics for given regions

Description

Usage

Arguments

Value

See Also