\HeaderA{readSpotTypes}{Read Spot Types File}{readSpotTypes}
\keyword{IO}{readSpotTypes}
\begin{Description}\relax
Read a table giving regular expressions to identify different types of spots in the gene-dataframe.
\end{Description}
\begin{Usage}
\begin{verbatim}
readSpotTypes(file="SpotTypes.txt",path=NULL,sep="\t",check.names=FALSE,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{file}] character string giving the name of the file specifying the spot types.
\item[\code{path}] character string giving the directory containing the file.
Can be omitted if the file is in the current working irectory.
\item[\code{sep}] the field separator character
\item[\code{check.names}] logical, if \code{FALSE} column names will not be converted to valid variable names, for example spaces in column names will not be left as is
\item[\code{...}] any other arguments are passed to \code{read.table}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The file is a text file with rows corresponding to types of spots and the following columns: \code{SpotType} gives the name for the spot type, \code{ID} is a regular expression matching the ID column, \code{Name} is a regular expression matching the Name column, and \code{Color} is the R name for the color to be associated with this type.
\end{Details}
\begin{Value}
A data frame with columns
\begin{ldescription}
\item[\code{SpotType}] character vector giving names of the spot types
\item[\code{ID}] character vector giving regular expressions
\item[\code{Name}] character vector giving regular expressions
\item[\code{Color}] character vector giving names of colors
\end{ldescription}
\end{Value}
\begin{Author}\relax
Gordon Smyth following idea of James Wettenhall
\end{Author}
\begin{SeeAlso}\relax
An overview of LIMMA functions for reading data is given in \LinkA{03.ReadingData}{03.ReadingData}.
\end{SeeAlso}

