aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/checksubstance.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/reference/checksubstance.html')
-rw-r--r--docs/reference/checksubstance.html176
1 files changed, 176 insertions, 0 deletions
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
new file mode 100644
index 0000000..0fbca62
--- /dev/null
+++ b/docs/reference/checksubstance.html
@@ -0,0 +1,176 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Check raw data for a specified substance — checksubstance • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">drfit</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <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>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>

Contact - Imprint