karyogram2

Functions for visualising IBD segments in karyograms. The <code>karyogram1()</code> and
<code>karyogram2()</code> functions produces karyograms illustrating the output of
<code>ibdsim()</code> for one or two specified individuals. The actual plotting is done
by functions <code>karyoHaploid()</code> and <code>karyoDiploid()</code>.

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 'ped suite' collection of packages for pedigree analysis.
A detailed presentation of the 'ped suite', 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

karyogram2 function

<dl><dt>sim</dt>
<dd>A <code>genomeSim</code> object.</dd>
<dt>ids</dt>
<dd>A vector of one or two ID labels.</dd>
<dt>verbose</dt>
<dd>A logical.</dd>
<dt>...</dt>
<dd>Further arguments passed on to <code>karyoHaploid()</code>.</dd></dl>

Arguments

Karyogram plots — karyogram2

<dl>

<dt>sim</dt>
<dd>A <code>genomeSim</code> object.</dd>


<dt>ids</dt>
<dd>A vector of one or two ID labels.</dd>


<dt>verbose</dt>
<dd>A logical.</dd>


<dt>...</dt>
<dd>Further arguments passed on to <code>karyoHaploid()</code>.</dd>

</dl>

karyogram2: Karyogram plots

Description

Usage

Value

Arguments

Examples