spline_IBD

Fits splines to IBD probabilities at a grid of positions at user-defined spacing.

Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.

Peter Bourke

polyqtlR

QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Christine Hackett

Chris Maliepaard

Geert van Geest

Roeland Voorrips

Johan Willemsen

spline_IBD function

<dl><dt>IBD_list</dt>
<dd>List of IBD probabilities</dd>
<dt>gap</dt>
<dd>The size (in centiMorgans) of the gap between splined positions</dd>
<dt>method</dt>
<dd>One of two options, either "linear" or "cubic". The default method (cubic) fits cubic splines, and although more accurate,
becomes computationally expensive in higher-density data-sets, where the linear option may be preferable.</dd>
<dt>ncores</dt>
<dd>Number of cores to use, by default 1 only. Works both for Windows and UNIX (using <code>doParallel</code>).
Use <code><a href="/link/parallel%3A%3AdetectCores()?package=polyqtlR&version=0.1.1" data-mini-rdoc="polyqtlR::parallel::detectCores()">parallel::detectCores()</a></code> to find out how many cores you have available. Note that with large datasets, using multiple cores
will use large amounts of memory (RAM). Single-core or e.g. 2-core evaluations, although slower, is less memory-intensive.</dd>
<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If <code>NULL</code> log is send to stdout.</dd></dl>

Arguments

Fit splines to IBD probabilities — spline_IBD

<dl>

<dt>IBD_list</dt>
<dd>List of IBD probabilities</dd>


<dt>gap</dt>
<dd>The size (in centiMorgans) of the gap between splined positions</dd>


<dt>method</dt>
<dd>One of two options, either "linear" or "cubic". The default method (cubic) fits cubic splines, and although more accurate,
becomes computationally expensive in higher-density data-sets, where the linear option may be preferable.</dd>


<dt>ncores</dt>
<dd>Number of cores to use, by default 1 only. Works both for Windows and UNIX (using <code>doParallel</code>).
Use <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> to find out how many cores you have available. Note that with large datasets, using multiple cores
will use large amounts of memory (RAM). Single-core or e.g. 2-core evaluations, although slower, is less memory-intensive.</dd>


<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If <code>NULL</code> log is send to stdout.</dd>

</dl>

spline_IBD: Fit splines to IBD probabilities

Description

Usage

Value

Arguments

Examples