\HeaderA{readCodelink}{Read Codelink Bioarrays Data}{readCodelink}
\keyword{documentation}{readCodelink}
\keyword{utilities}{readCodelink}
\begin{Description}\relax
Read data exported as text by Codelink Software. It reads values (normalized
by Codelink Software or not) flags and information about probes.
\end{Description}
\begin{Usage}
\begin{verbatim}
    readCodelink(files=list.files(pattern="TXT"), sample.name=NULL,
        flag, dec=NULL, type="Spot",    preserve=FALSE, verbose=2,
        file.type="Codelink", check=TRUE, fix=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{files}] list of files to read.
\item[\code{sample.name}] vector of same length as files with sample names.
\item[\code{flag}] list with values to assign based on Flag quality values.
\item[\code{dec}] character indicating the decimal character used in the files.
\item[\code{type}] character indicating which base value to read from files.
\item[\code{preserve}] logical, if TRUE Bkgd\_stdev slot is not removed (if present).
\item[\code{verbose}] numerical, set the level of information. Level 2 set as old behaviour. Level > 2 output some debug info.
\item[\code{file.type}] exported file type, currently Codelink or XLS file formats supported.
\item[\code{check}] logical, check for probe order consistency.
\item[\code{fix}] logical, try to fix probe order consistency.
\end{ldescription}
\end{Arguments}
\begin{Value}
An object of class "Codelink".
\end{Value}
\begin{Author}\relax
Diego Diez
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{read.table}{read.table}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
    # reading default extension (TXT).
    data <- readCodelink()

    # specify a different one.
    files <- list.files(pattern = "txt")
    data <- readCodelink(files = files)

    # example.
    data(codelink.example)
## End(Not run)
\end{ExampleCode}
\end{Examples}

