MzQCsetQuality

MzQCsetQuality-class

<p>The object is an alias for MzQCbaseQuality.</p>

Reads, writes and validates 'mzQC' files. The 'mzQC' format is a
standardized file format for the exchange, transmission, and archiving of
quality metrics derived from biological mass spectrometry data, as defined
by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative)
Quality Control working group.
See <https://hupo-psi.github.io/mzQC/> for details.

Chris Bielow

rmzqc

Creation, Reading and Validation of 'mzqc' Files

David Jimenez-Morales

Jeremi Maciejewski

MzQCsetQuality function

<p><code>rmzqc::MzQCbaseQuality</code> -&gt; <code>MzQCsetQuality</code></p>

Super class


<div class="section" id="public-methods">
<h3>Public methods</h3><p></p><p><ul>
<li><p><a href="/link/MzQCsetQuality%24clone()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::MzQCsetQuality$clone()"><code>MzQCsetQuality$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="rmzqc" data-topic="MzQCbaseQuality" data-id="fromData"><a href="/link/rmzqc%3A%3AMzQCbaseQuality%24fromData()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::rmzqc::MzQCbaseQuality$fromData()"><code>rmzqc::MzQCbaseQuality$fromData()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="getMetric"><a href="/link/rmzqc%3A%3AMzQCbaseQuality%24getMetric()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::rmzqc::MzQCbaseQuality$getMetric()"><code>rmzqc::MzQCbaseQuality$getMetric()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="initialize"><a href="/link/rmzqc%3A%3AMzQCbaseQuality%24initialize()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::rmzqc::MzQCbaseQuality$initialize()"><code>rmzqc::MzQCbaseQuality$initialize()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="isValid"><a href="/link/rmzqc%3A%3AMzQCbaseQuality%24isValid()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::rmzqc::MzQCbaseQuality$isValid()"><code>rmzqc::MzQCbaseQuality$isValid()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="toJSON"><a href="/link/rmzqc%3A%3AMzQCbaseQuality%24toJSON()?package=rmzqc&version=0.7.0" data-mini-rdoc="rmzqc::rmzqc::MzQCbaseQuality$toJSON()"><code>rmzqc::MzQCbaseQuality$toJSON()</code></a></span></li>
</ul>
</details></p><p><hr>
<a id="method-MzQCsetQuality-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>MzQCsetQuality$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

A setQuality object. Use it for metrics which are specific to sets, i.e. only for values which
only make sense in the set context and cannot be stored as runQuality (see mzQC spec doc). — MzQCsetQuality


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

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

</div><p><details open><summary>Inherited methods</summary>
<ul>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="fromData"><a href='../../rmzqc/html/MzQCbaseQuality.html#method-MzQCbaseQuality-fromData'><code>rmzqc::MzQCbaseQuality$fromData()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="getMetric"><a href='../../rmzqc/html/MzQCbaseQuality.html#method-MzQCbaseQuality-getMetric'><code>rmzqc::MzQCbaseQuality$getMetric()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="initialize"><a href='../../rmzqc/html/MzQCbaseQuality.html#method-MzQCbaseQuality-initialize'><code>rmzqc::MzQCbaseQuality$initialize()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="isValid"><a href='../../rmzqc/html/MzQCbaseQuality.html#method-MzQCbaseQuality-isValid'><code>rmzqc::MzQCbaseQuality$isValid()</code></a></span></li>
<li><span class="pkg-link" data-pkg="rmzqc" data-topic="MzQCbaseQuality" data-id="toJSON"><a href='../../rmzqc/html/MzQCbaseQuality.html#method-MzQCbaseQuality-toJSON'><code>rmzqc::MzQCbaseQuality$toJSON()</code></a></span></li>
</ul>
</details>

<hr>
<a id="method-MzQCsetQuality-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>MzQCsetQuality$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>


A setQuality object. Use it for metrics which are specific to sets, i.e. only for values which
only make sense in the set context and cannot be stored as runQuality (see mzQC spec doc).

MzQCsetQuality: A setQuality object. Use it for metrics which are specific to sets, i.e. only for values which only make sense in the set context and cannot be stored as runQuality (see mzQC spec doc).

Description

Arguments

Super class

Methods

Public methods

Method `clone()`

Usage

Arguments

Description

Arguments

Super class

Methods

Public methods

Method clone()

Usage

Arguments

Method `clone()`