\HeaderA{readGenes.pfizer}{Read genetics data files that use Pfizer's data format.}{readGenes.pfizer}
\keyword{misc}{readGenes.pfizer}
\begin{Description}\relax
Read genetics data files that use Pfizer's data format.
\end{Description}
\begin{Usage}
\begin{verbatim}
readGenes.pfizer(filename, phase=list(F),
                 format=c("Pivot", "Listing"),...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{filename}] Name of the file in which data is stored 
\item[\code{phase}] see below
\item[\code{format}] Format of the file to be read, one of "Pivot" or "Listing"
\item[\code{...}] Additional arguments to function read.table
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The argument \code{phase} may be:
\Enumerate{
\item[1] A single logical scalar value that applies for all markers
\item[2] A logical vector with one element per marker
\item[3] A phaseObject (TBD) providing observation by marker by phase
probabilities + definitions of contigs + probability of
contigs

}
\end{Details}
\begin{Value}
a geneSet object
\end{Value}
\begin{Author}\relax
Gregory R. Warnes \email{warnes@bst.rochester.edu}
and
Nitin Jain \email{nitin.jain@pfizer.com}
\end{Author}
\begin{Examples}
\begin{ExampleCode}

# store where we are now
here <- getwd()

# move to the data directory
dir <- file.path(.path.package("GeneticsBase"),"data")
setwd(dir)

# load Pfizer Data
PfizerExample <- readGenes.pfizer("PfizerExample.txt", format="Listing")

# look at the data
PfizerExample

# return to the original path
setwd(here)

\end{ExampleCode}
\end{Examples}

