plotLOAF

Plots all (sorted by increasing value) observed PMR values with
maximum posterior probability classifications represented by colour
and shape.
Options include a cut off for the minimum number of overlapping SNPs,
the max number of pairs to plot and x-axis font size.

The goal of the package is to provide an easy-to-use method
for estimating degrees of relatedness (up to the second degree)
for extreme low-coverage data. The package also allows users to
quantify and visualise the level of confidence in the estimated
degrees of relatedness.

Jonathan Tuke

BREADR

Estimates Degrees of Relatedness (Up to the Second Degree) for
Extreme Low-Coverage Data

Jono Tuke

Adam B. Rohrlach

Wolfgang Haak

Divyaratan Popli

plotLOAF function

<dl><dt>in_tibble</dt>
<dd>a tibble that is the output of the callRelatedness() function.</dd>
<dt>nsnps_cutoff</dt>
<dd>the minimum number of overlapping SNPs for which
pairs are removed from the plot. If NULL, default is 500.</dd>
<dt>N</dt>
<dd>the number of (sorted by increasing PMR) pairs to plot.
Avoids plotting all pairs (many of which are unrelated).</dd>
<dt>fntsize</dt>
<dd>the fontsize for the x-axis names.</dd>
<dt>verbose</dt>
<dd>if TRUE, then information about the plotting process is sent
to the console</dd></dl>

Arguments

plotLOAF — plotLOAF

<dl>

<dt>in_tibble</dt>
<dd>a tibble that is the output of the callRelatedness() function.</dd>


<dt>nsnps_cutoff</dt>
<dd>the minimum number of overlapping SNPs for which
pairs are removed from the plot. If NULL, default is 500.</dd>


<dt>N</dt>
<dd>the number of (sorted by increasing PMR) pairs to plot.
Avoids plotting all pairs (many of which are unrelated).</dd>


<dt>fntsize</dt>
<dd>the fontsize for the x-axis names.</dd>


<dt>verbose</dt>
<dd>if TRUE, then information about the plotting process is sent
to the console</dd>

</dl>

plotLOAF: plotLOAF

Description

Usage

Value

Arguments

Examples