oligoType

Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) and transforms to the appropriate formats of
the 'qpcR' and 'chipPCR' packages, as described in Rodiger et al. (2017) <doi:10.1093/bioinformatics/btx528>.
Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.

Konstantin A Blagodatskikh

RDML

Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files

Konstantin Blagodatskikh

Stefan Roediger

Michal Burdukiewicz

Andrej-Nikolai Spiess

oligoType function

<p>An <code><a href="https://r6.r-lib.org/reference/R6Class.html">R6Class</a></code> generator object.</p>

Format

<p></p><pre><code>oligoType$new(threePrimeTag = NULL,
  fivePrimeTag = NULL, sequence)</code></pre><p></p><p></p><p>@section Fields:</p><dl>
  <dt><code>threePrimeTag</code></dt>
<dd><p><a href="/link/checkString?package=RDML&version=1.1" data-mini-rdoc="RDML::checkString">checkString</a>. Description of
  three prime modification (if present).</p></dd><p></p><p>  <dt><code>fivePrimeTag</code></dt>
<dd><p><a href="/link/checkString?package=RDML&version=1.1" data-mini-rdoc="RDML::checkString">checkString</a>. Description of
  five prime modification (if present).</p></dd></p><p>  <dt><code>sequence</code></dt>
<dd><p><a href="/link/checkString?package=RDML&version=1.1" data-mini-rdoc="RDML::checkString">checkString</a>.</p></dd></p><p>  
</p></dl>


Initialization

<p><code>RDML::rdmlBaseType</code> -&gt; <code>oligoType</code></p>

Super class


<div class="section" id="public-methods">
<h3>Public methods</h3><p></p><p><ul>
<li><p><a href="/link/oligoType%24new()?package=RDML&version=1.1" data-mini-rdoc="RDML::oligoType$new()"><code>oligoType$new()</code></a></p></li>
<li><p><a href="/link/oligoType%24clone()?package=RDML&version=1.1" data-mini-rdoc="RDML::oligoType$clone()"><code>oligoType$clone()</code></a></p></li>
</ul></p><p></p></div><p><details open><summary>Inherited methods</summary>
<ul>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id=".asXMLnodes"><a href="/link/RDML%3A%3ArdmlBaseType%24.asXMLnodes()?package=RDML&version=1.1" data-mini-rdoc="RDML::RDML::rdmlBaseType$.asXMLnodes()"><code>RDML::rdmlBaseType$.asXMLnodes()</code></a></span></li>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id="copy"><a href="/link/RDML%3A%3ArdmlBaseType%24copy()?package=RDML&version=1.1" data-mini-rdoc="RDML::RDML::rdmlBaseType$copy()"><code>RDML::rdmlBaseType$copy()</code></a></span></li>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id="print"><a href="/link/RDML%3A%3ArdmlBaseType%24print()?package=RDML&version=1.1" data-mini-rdoc="RDML::RDML::rdmlBaseType$print()"><code>RDML::rdmlBaseType$print()</code></a></span></li>
</ul>
</details></p><p><hr>
<a id="method-oligoType-new"></a></p><div class="section" id="method-new-">
<h3>Method <code>new()</code></h3><p></p><p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>oligoType$new(threePrimeTag = NULL, fivePrimeTag = NULL, sequence)</code></pre><p></p></div></p>
</div><p></p><p>
</p><p><hr>
<a id="method-oligoType-clone"></a></p><div class="section" id="method-clone-">
<h3>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><div class="section" id="usage">
<h4>Usage</h4>
<p><div class="r"></div></p><pre><code>oligoType$clone(deep = FALSE)</code></pre><p></p></div><p></p>
</div><p></p><p><div class="section" id="arguments">
<h4>Arguments</h4>
<p><div class="arguments"></div></p><dl>
<dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd></dl></div></p><p>
</p><p></p>
<p></p><p>
</p>

Methods

oligoType R6 class. — oligoType

<p>An <code><a href='https://r6.r-lib.org/reference/R6Class.html'>R6Class</a></code> generator object.</p>

<p></p><pre><code>oligoType$new(threePrimeTag = NULL,
  fivePrimeTag = NULL, sequence)</code></pre>

<p>@section Fields:</p><dl>
  <dt><code>threePrimeTag</code></dt>
<dd><p><a href='https://rdrr.io/pkg/checkmate/man/checkString.html'>checkString</a>. Description of
  three prime modification (if present).</p></dd>

  <dt><code>fivePrimeTag</code></dt>
<dd><p><a href='https://rdrr.io/pkg/checkmate/man/checkString.html'>checkString</a>. Description of
  five prime modification (if present).</p></dd>

  <dt><code>sequence</code></dt>
<dd><p><a href='https://rdrr.io/pkg/checkmate/man/checkString.html'>checkString</a>.</p></dd>

  
</dl>



<div class='section' id='public-methods'>
<h3>Public methods</h3>

<ul>
<li><p><a href='#method-oligoType-new'><code>oligoType$new()</code></a></p></li>
<li><p><a href='#method-oligoType-clone'><code>oligoType$clone()</code></a></p></li>
</ul>

</div><p><details open><summary>Inherited methods</summary>
<ul>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id=".asXMLnodes"><a href='../../RDML/html/rdmlBaseType.html#method-rdmlBaseType-.asXMLnodes'><code>RDML::rdmlBaseType$.asXMLnodes()</code></a></span></li>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id="copy"><a href='../../RDML/html/rdmlBaseType.html#method-rdmlBaseType-copy'><code>RDML::rdmlBaseType$copy()</code></a></span></li>
<li><span class="pkg-link" data-pkg="RDML" data-topic="rdmlBaseType" data-id="print"><a href='../../RDML/html/rdmlBaseType.html#method-rdmlBaseType-print'><code>RDML::rdmlBaseType$print()</code></a></span></li>
</ul>
</details>

<hr>
<a id="method-oligoType-new"></a></p><div class='section' id='method-new-'>
<h3>Method <code>new()</code></h3>

<div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>oligoType$new(threePrimeTag = NULL, fivePrimeTag = NULL, sequence)</code></pre><p></div></p>
</div>


</div><p><hr>
<a id="method-oligoType-clone"></a></p><div class='section' id='method-clone-'>
<h3>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><div class='section' id='usage'>
<h4>Usage</h4>
<p><div class="r"></p><pre><code>oligoType$clone(deep = FALSE)</code></pre><p></div></p>
</div>

<div class='section' id='arguments'>
<h4>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>


</dl><p></div></p>
</div>

</div>


oligoType: oligoType R6 class.

Description

Arguments

Format

Initialization

Super class

Methods

Public methods

Method `new()`

Usage

Method `clone()`

Usage

Arguments

Description

Arguments

Format

Initialization

Super class

Methods

Public methods

Method new()

Usage

Method clone()

Usage

Arguments

Method `new()`

Method `clone()`