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<h1>ZINB-WaVE simulation</h1>
<small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/zinb-simulate.R'><code>R/zinb-simulate.R</code></a></small>
<div class="hidden name"><code>zinbSimulate.Rd</code></div>
</div>
<div class="ref-description">
<p>Simulate counts using the ZINB-WaVE method.</p>
</div>
<pre class="usage"><span class='fu'>zinbSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>params</th>
<td><p>ZINBParams object containing simulation parameters.</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>logical. Whether to print progress messages</p></td>
</tr>
<tr>
<th>...</th>
<td><p>any additional parameter settings to override what is provided in
<code>params</code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> that
takes a <code><a href='ZINBParams.html'>ZINBParams</a></code>, runs the simulation then converts the
output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
See <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> and the ZINB-WaVE paper for
more details about how the simulation works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
and environmental backgrounds across single-cells and populations. bioRxiv
(2017).</p>
<p>Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert J-P. ZINB-WaVE: A general
and flexible method for signal extraction from single-cell RNA-seq data
bioRxiv (2017).</p>
<p>Paper: <a href='10.1101/125112'>10.1101/125112</a></p>
<p>Code: <a href='https://github.com/drisso/zinbwave'>https://github.com/drisso/zinbwave</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>zinbSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'>
</div></pre>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#references">References</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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