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diff --git a/man/drdata.Rd b/man/drdata.Rd new file mode 100644 index 0000000..b9f8660 --- /dev/null +++ b/man/drdata.Rd @@ -0,0 +1,74 @@ +\name{drdata} +\alias{drdata} +\title{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{ + \item{substances}{ + A string or an array of strings with the substance names for + which dose-response data is to be retrieved.} + \item{experimentator}{ + The name of the experimentator whose data is to be used.} + \item{db}{ + The database to be used. Currently only "cytotox" of the UFT Department of + Bioorganic Chemistry is supported.} + \item{celltype}{ + Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.} + \item{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).} + \item{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{ + \item{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. + 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 \file{/etc/odbcinst.ini} + containing: + \tabular{lll}{ + [MySQL] \tab \tab \cr + Description \tab = \tab MySQL driver for ODBC \cr + Driver \tab = \tab /usr/local/lib/libmyodbc.so \cr + Setup \tab = \tab /usr/lib/odbc/libodbcmyS.so \cr + } + and the file \file{/etc/odbc.ini} containing: + \tabular{lll}{ + [cytotox] \tab \tab \cr + Description \tab = \tab Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen \cr + Driver \tab = \tab MySQL \cr + Trace \tab = \tab Yes \cr + TraceFile \tab = \tab /tmp/odbc.log \cr + Database \tab = \tab cytotox \cr + Server \tab = \tab eckehaat \cr + Port \tab = \tab 3306 \cr + }. +} +\examples{ +# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells +\dontrun{data <- drdata(c("TBT","Zn Pyrithion"))} +} +\author{ + Johannes Ranke + \email{jranke@uni-bremen.de} + \url{http://www.uft.uni-bremen.de/chemie/ranke} +} +\keyword{IO} +\keyword{database} |