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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
commitae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree61bc66f752a81e9d50becf173d138ca9dfa80778 /docs/reference/checksubstance.html
parentcd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)
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+ <h1>Check raw data for a specified substance</h1>
+ </div>
+
+
+ <p>Report metadata for a specified substance from a specified database, and plot
+ the data.</p>
+
+
+ <pre><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+ <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+ <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+ <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</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>substance</th>
+ <td><p>The name of the substance identifying it within the database.</p></td>
+ </tr>
+ <tr>
+ <th>db</th>
+ <td><p>The database to be used. Currently, the databases "cytotox" and "enzymes"
+ of the UFT Department of Bioorganic Chemistry are supported (default is
+ "cytotox").</p></td>
+ </tr>
+ <tr>
+ <th>experimentator</th>
+ <td><p>The name of the experimentator whose data is to be used. Default is "%",
+ which means that data from all experimentators are shown.</p></td>
+ </tr>
+ <tr>
+ <th>celltype</th>
+ <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+ supported. Default is "%", i.e. data for any cell type will be
+ displayed.</p></td>
+ </tr>
+ <tr>
+ <th>enzymetype</th>
+ <td><p>Currently, only data for AChE, GR and GST are supported. The default value
+ is "%", i.e. data for any enzyme type will be displayed.</p></td>
+ </tr>
+ <tr>
+ <th>organism</th>
+ <td><p>The latin name of the tested organism, if the ecotox db was selected. The
+ default value is "%", i.e. data for any organism will be displayed.</p></td>
+ </tr>
+ <tr>
+ <th>endpoint</th>
+ <td><p>The endpoint that should be used for selecting the data. Only important if
+ the database "ecotox" is used. Defaults to "%".</p></td>
+ </tr>
+ <tr>
+ <th>whereClause</th>
+ <td><p>With this argument, additional conditions for the SQL query can be set,
+ e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).</p></td>
+ </tr>
+ <tr>
+ <th>ok</th>
+ <td><p>With the default value "%", all data in the database is retrieved for the
+ specified substance.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function lists a report and shows one graph.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Check substance IM14 BF4 in the cytotox database</span>
+<span class='co'>## Not run: checksubstance("IM14 BF4")</span></div></pre>
+ </div>
+ <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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
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