drdata: Get dose-response data via RODBC

Description Usage Arguments Details Value Author(s) Examples

View source: R/drdata.R

Description

Get dose-response data from an adequate ODBC data source

Usage

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  drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
    enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
    whereClause = "1", ok = "'ok','no fit'")

Arguments

substances

A string or an array of strings with the substance names for which dose-response data is to be retrieved. Matching is case-sensitive.

experimentator

The name of the experimentator whose data is to be used. Default is " which means that data from all experimentators are retrieved.

db

The database to be used. Currently, the databases "cytotox", "enzymes" and "ecotox" 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.

organism

The organism that was exposed to the chemical. Only important if the database "ecotox" is used. Defaults to "Vibrio fischeri".

endpoint

The endpoint that should be used for selecting the data. Only important if the database "ecotox" is used. Defaults to "Luminescence".

whereClause

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).

ok

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.

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 [email protected] http://www.uft.uni-bremen.de/chemie/ranke

Examples

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# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
# cells
## Not run: drdata(c("TBT","ZnPT2"))

drfit documentation built on July 19, 2017, 9:02 a.m.