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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
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+ <h1>Get dose-response data via RODBC</h1>
+ </div>
+
+
+ <p>Get dose-response data from an adequate ODBC data source</p>
+
+
+ <pre><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>,
+ <span class='kw'>enzymetype</span><span class='kw'>=</span><span class='st'>"AChE"</span>, <span class='kw'>organism</span><span class='kw'>=</span><span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span><span class='kw'>=</span><span class='st'>"Luminescence"</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'>"'ok','no fit'"</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>substances</th>
+ <td><p>A string or an array of strings with the substance names for
+ which dose-response data is to be retrieved.</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 retrieved.</p></td>
+ </tr>
+ <tr>
+ <th>db</th>
+ <td><p>The database to be used. Currently, the databases "cytotox", "enzymes"
+ and "ecotox" of the UFT Department of Bioorganic Chemistry are
+ supported (default is "cytotox").</p></td>
+ </tr>
+ <tr>
+ <th>celltype</th>
+ <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+ supported.</p></td>
+ </tr>
+ <tr>
+ <th>enzymetype</th>
+ <td><p>Currently, only data for AChE, GR and GST are supported.</p></td>
+ </tr>
+ <tr>
+ <th>organism</th>
+ <td><p>The organism that was exposed to the chemical. Only important if the database
+ "ecotox" is used. Defaults to "Vibrio fischeri".</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 "Luminescence".</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" (i.e. "Do not retrieve data for 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 "'ok','no fit'", only data that has been checked and
+ set to "ok" or "no fit" in the database is retrieved. The argument "no fit"
+ will result in not using the data for fitting, but it will be plotted.
+ Another sensible argument would be "'ok','no fit','?'", in order to
+ additionally retrieve data which has not yet been checked.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p></p>
+<dt>data</dt><dd><p>A data frame with a factor describing the dose levels, the numeric dose
+ levels and a numeric column describing the response, as well as the entries
+ for plate, experimentator, performed (date of test performance), celltype,
+ unit (of the dose/concentration), and for the ok field in the database.</p></dd>
+
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The function is currently only used for retrieving data from the
+ mysql database "cytotox" of the UFT Department of Bioorganic Chemistry.
+ Access to this database is limited to UFT staff. Additionally to the
+ installation of the RODBC package, it is required to set up a ODBC data
+ source with the name "cytotox", using an ODBC driver for mysql, probably
+ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the
+ respective data source with data source name (DSN) "cytotox". For my
+ setting using unixodbc, I am using the file <code class="file">/etc/odbcinst.ini</code>
+ containing:</p><table><tr><td>
+ [MySQL] </td>
+<td> </td>
+</tr><tr><td> </td>
+<td>
+ Description </td>
+</tr><tr><td> = </td>
+<td> MySQL driver for ODBC </td>
+</tr><tr><td>
+ Driver </td>
+<td> = </td>
+</tr><tr><td> /usr/local/lib/libmyodbc.so </td>
+<td>
+ Setup </td>
+</tr><tr><td> = </td>
+<td> /usr/lib/odbc/libodbcmyS.so </td>
+</tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table><tr><td>
+ [cytotox] </td>
+<td> </td>
+</tr><tr><td> </td>
+<td>
+ Description </td>
+</tr><tr><td> = </td>
+<td> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
+</tr><tr><td>
+ Driver </td>
+<td> = </td>
+</tr><tr><td> MySQL </td>
+<td>
+ Trace </td>
+</tr><tr><td> = </td>
+<td> Yes </td>
+</tr><tr><td>
+ TraceFile </td>
+<td> = </td>
+</tr><tr><td> /tmp/odbc.log </td>
+<td>
+ Database </td>
+</tr><tr><td> = </td>
+<td> cytotox </td>
+</tr><tr><td>
+ Server </td>
+<td> = </td>
+</tr><tr><td> eckehaat </td>
+<td>
+ Port </td>
+</tr><tr><td> = </td>
+<td> 3306 </td>
+</tr></table>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span>
+<span class='co'># cells</span>
+<span class='co'>## Not run: drdata(c("TBT","ZnPT2"))</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="#details">Details</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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