\HeaderA{PRv9mers}{Print Run Quality version 9mers}{PRv9mers}
\keyword{hplot}{PRv9mers}
\begin{Description}\relax
Qualitative diagnostic plots looking at print-run quality.  This
component examine the 9mers hybridizations.
\end{Description}
\begin{Usage}
\begin{verbatim}
PRv9mers(fnames, path = ".", dev = "png", DEBUG = FALSE, prargs = NULL, samepr = TRUE, prname = "xMm", save = TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fnames}] A "character" string naming the input files.
\item[\code{path}] A "character" string representing the data directory. By
default this is set to the current working directory (".").
\item[\code{dev}] A "character" string naming the graphics device. This will
take arguments "png", "jpeg" and "ps" only.
\item[\code{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{prargs}] A list with 4 components: Block, Row, Column and
ncolumns. See Details for more information.
\item[\code{samepr}] If 'TRUE', we assume everything in the directory are
from the same print-run.
\item[\code{prname}] A "character" string giving the name of the print-run.
\item[\code{save}] If `TRUE', the figures will be saved to files.
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The argument "prargs" is used to calculate the layout information
about a print-run.  Components Block, Row and Columns denote the
column names from the input data representing the print-tip location.
The component "ncolumns" is an integer representing the number of
print-tip columns in the data.  If the arguement is set to NULL,
the the following default will be used.  list(Block="Block",
Row="Row", Column="Column", ncolumns=4)
\end{Details}
\begin{Value}
Files of diagnostic plots and  excel files containings probe IDs of
problematic probes.
\end{Value}
\begin{Author}\relax
Jean Yee Hwa Yang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
datadir <- system.file("gprQCData", package="arrayQuality")
if (interactive())
PRv9mers(fnames="12Mm250.gpr", path=datadir, prname="12Mm")
\end{ExampleCode}
\end{Examples}

