\HeaderA{read.Galfile}{Reading GenePix Gal file}{read.Galfile}
\keyword{file}{read.Galfile}
\begin{Description}\relax
Reading a standard Gal file containing gene information.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.Galfile(galfile, path = ".", info.id = c("ID", "Name"),
layout.id =c(Block="Block", Row="Row", Column="Column"),
labels = "ID", notes = "", sep = "\t", skip = NULL,   ncolumns=4, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{galfile}] a character string representing the Gal file.
\item[\code{path}] a character string representing the data directory. By
default this is set to the current working directory ("."). 
\item[\code{info.id}] the column numbers or names in `fname' that contain the required
information.
\item[\code{layout.id}] the column names in `fname' that specified the
printer layout information.
\item[\code{labels}] the column number in \code{fname} which contains the names that the user would like to use to label spots or arrays (e.g. for default titles in \code{\LinkA{maPlot}{maPlot}}.
\item[\code{notes}] object of class character, vector of explanatory text
\item[\code{sep}] the field separator character.  Values on each line of the
file are separated by this character. The
default is to read a tab delimited file.
\item[\code{skip}] the number of lines of the data file to skip before
beginning to read data.
\item[\code{ncolumns}] an integer representing the number of columns of
sub-array (print-tips) on a slides.
\item[\code{...}] further arguments to \code{\LinkA{scan}{scan}}.
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{gnames}] An object of class \code{\LinkA{marrayInfo}{marrayInfo}}.
\item[\code{layout}] An object of class \code{\LinkA{marrayLayout}{marrayLayout}}.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Yee Hwa (Jean) Yang
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{read.marrayInfo}{read.marrayInfo}}, \code{\LinkA{read.marrayLayout}{read.marrayLayout}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
library(marray)
datadir <- system.file("swirldata", package="marray")
try <- read.Galfile(galfile="fish.gal", path=datadir)
names(try)
try$layout
try$gnames
\end{ExampleCode}
\end{Examples}