\HeaderA{readSpikeTypes}{Read Spike Types File}{readSpikeTypes}
\keyword{data}{readSpikeTypes}
\begin{Description}\relax
Read a table containing information about the doping control mixture used in
the hybridization.
\end{Description}
\begin{Usage}
\begin{verbatim}
readSpikeTypes(file = "DopingTypeFile2.txt", path = NULL, cy5col = "MassCy5", cy3col = "MassCy3", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{file}] A "character" string giving the name of the file specifying
the doping controls used.
\item[\code{path}] A "character" string giving the directory containing the
file. By default this is set to the current working directory
(".").
\item[\code{cy5col}] A "character" string describing the name of the column
corresponding to the controls labelled with Cy5.
\item[\code{cy3col}] A "character" string describing the name of the column
corresponding to the controls labelled with Cy3.
\item[\code{...}] Additional arguments passed to "readSpotTypes"
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The file is a text file with rows corresponding to doping controls
and columns describing various experimental conditions. It must
contain an oligo sequence identifier for each control, the spike type
(e.g. Ambion or MJ) and the mass of each oligo spiked in each
channel. By default, this function assumes that the mass unit are the same.
\end{Details}
\begin{Value}
A list of n matrices, each matrix containing information about a unique
type of spiked controls.
\end{Value}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{Examples}
\begin{ExampleCode}
datadir <- system.file("Meebo", package="arrayQuality")
if (interactive())
{
spikes <-
readSpikeTypes(file="StanfordDCV1.7complete.txt",path=datadir,cy5col="CY5.ng._MjDC_V1.7",cy3col="CY3.ng._MjDC_V1.7")
}
\end{ExampleCode}
\end{Examples}

