drfit (version 0.03-13)

drdata: Get dose-response data

Description

Get dose-response data from a remote mysql server

Usage

drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81", 
    enzymetype="AChE", 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. Default is " means that data from all experimentators are retrieved.

db

The database to be used. Currently, the databases "cytotox" and "enzymes" of the UFT Department of Bioorganic Chemistry are supported (default is "cytotox").

celltype

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.

enzymetype

Currently, only data for AChE, GR and GST 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.

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.

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: lll{ [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: lll{ [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 }.

Examples

# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
data <- drdata(c("TBT","Zn Pyrithion"))