drdata(drfit)R Documentation

Get dose-response data

Description

Get dose-response data from a remote mysql server

Usage

  drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81", 
    whereClause = "1", ok = "'ok'")

Arguments

substances A string or an array of strings with the substance names for which dose-response data is to be retrieved.
experimentator The name of the experimentator whose data is to be used.
db The database to be used. Currently only "cytotox" of the UFT Department of Bioorganic Chemistry is supported.
celltype Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.
whereClause 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).
ok 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.

Details

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 ‘/etc/odbcinst.ini’ containing:
[MySQL]
Description = MySQL driver for ODBC
Driver = /usr/local/lib/libmyodbc.so
Setup = /usr/lib/odbc/libodbcmyS.so

and the file ‘/etc/odbc.ini’ containing:
[cytotox]
Description = Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
Driver = MySQL
Trace = Yes
TraceFile = /tmp/odbc.log
Database = cytotox
Server = eckehaat
Port = 3306
.

Value

data 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.

Author(s)

Johannes Ranke jranke@uni-bremen.de http://www.uft.uni-bremen.de/chemie/ranke

Examples

# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
## Not run: data <- drdata(c("TBT","Zn Pyrithion"))
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