legacy_decode19

A legacy version of the built-in human recombination map, based on
Halldorsson et al., 2019. The implementation of this map used in ibdsim2 was
updated in v2.3.0, adding the physical endpoint of each chromosome (this was
previously lacking), and using a better thinning algorithm to reduce the raw
data given by Halldorsson et al. (2019). See also <code>loadMap()</code>.

datasets

Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.

Magnus Vigeland

ibdsim2

Simulation of Chromosomal Regions Shared by Family Members

Magnus Dehli Vigeland

legacy_decode19 function

A <code>genomeMap</code> object: a list of 23 <code>chromMap</code> objects. Each
<code>chromMap</code> is a list containing two numeric matrices, named <code>male</code> and
<code>female</code>, and carries these attributes:<ul>
<li><code>physStart</code> - first physical position (Mb) on the chromosome</li>
<li><code>physEnd</code> - last physical position (Mb) on the chromosome</li>
<li><code>physRange</code> - physical length, <code>physEnd - physStart</code> (Mb)</li>
<li><code>mapLen</code> - length-2 numeric: centiMorgan length of male and female strands</li>
<li><code>chrom</code> - chromosome label</li>
<li><code>Xchrom</code> - logical flag used by simulators for X-inheritance</li>
</ul>

legacy_decode19: Legacy version of the `decode19` map

Description

Usage

Arguments

Format

Examples