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| author | (no author) <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc> | 2004-07-27 07:36:01 +0000 |
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| committer | (no author) <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc> | 2004-07-27 07:36:01 +0000 |
| commit | 8154a03c79eb910c42dcff03fd8fa611cdc8cc9d (patch) | |
| tree | c4e64967d78078a0fb0a8c9ec85307c35c9ec8f9 /chm/drdata.html | |
First version published on CRAN
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@1 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
Diffstat (limited to 'chm/drdata.html')
| -rw-r--r-- | chm/drdata.html | 146 |
1 files changed, 146 insertions, 0 deletions
diff --git a/chm/drdata.html b/chm/drdata.html new file mode 100644 index 0000000..7dd4a2b --- /dev/null +++ b/chm/drdata.html @@ -0,0 +1,146 @@ +<html><head><title>Get dose-response data</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drdata(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drdata">
+<param name="keyword" value=" Get dose-response data">
+</object>
+
+
+<h2>Get dose-response data</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Get dose-response data from a remote mysql server
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
+ whereClause = "1", ok = "'ok'")
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>substances</code></td>
+<td>
+A string or an array of strings with the substance names for
+which dose-response data is to be retrieved.</td></tr>
+<tr valign="top"><td><code>experimentator</code></td>
+<td>
+The name of the experimentator whose data is to be used.</td></tr>
+<tr valign="top"><td><code>db</code></td>
+<td>
+The database to be used. Currently only "cytotox" of the UFT Department of
+Bioorganic Chemistry is supported.</td></tr>
+<tr valign="top"><td><code>celltype</code></td>
+<td>
+Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.</td></tr>
+<tr valign="top"><td><code>whereClause</code></td>
+<td>
+With this argument, additional conditions for the SQL query can be set,
+e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).</td></tr>
+<tr valign="top"><td><code>ok</code></td>
+<td>
+With the default value "'ok'", only data that has been checked and set to "ok"
+in the database is retrieved. Another sensible argument would be "'ok','?'", in
+order to additionally retrieve data which has not yet been checked.</td></tr>
+</table>
+
+<h3>Details</h3>
+
+<p>
+The function is currently only used for retrieving data from the
+mysql database "cytotox" of the UFT Department of Bioorganic Chemistry.
+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 ‘<TT>/etc/odbcinst.ini</TT>’
+containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[MySQL] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> MySQL driver for ODBC </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> /usr/local/lib/libmyodbc.so </td>
+</tr>
+<tr>
+ <td align="left"> Setup </td> <td align="left"> = </td> <td align="left"> /usr/lib/odbc/libodbcmyS.so </td>
+</tr>
+</table>
+<p>
+and the file ‘<TT>/etc/odbc.ini</TT>’ containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[cytotox] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> MySQL </td>
+</tr>
+<tr>
+ <td align="left"> Trace </td> <td align="left"> = </td> <td align="left"> Yes </td>
+</tr>
+<tr>
+ <td align="left"> TraceFile </td> <td align="left"> = </td> <td align="left"> /tmp/odbc.log </td>
+</tr>
+<tr>
+ <td align="left"> Database </td> <td align="left"> = </td> <td align="left"> cytotox </td>
+</tr>
+<tr>
+ <td align="left"> Server </td> <td align="left"> = </td> <td align="left"> eckehaat </td>
+</tr>
+<tr>
+ <td align="left"> Port </td> <td align="left"> = </td> <td align="left"> 3306 </td>
+</tr>
+</table>
+.
+</p>
+
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>data</code></td>
+<td>
+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.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+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>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
+## Not run: data <- drdata(c("TBT","Zn Pyrithion"))
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
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