\HeaderA{gwSnpScreenResult-class}{Class "gwSnpScreenResult" -- container for GGtools gwSnpScreen
method outputs and allied objects}{gwSnpScreenResult.Rdash.class}
\aliasA{cwSnpScreenResult-class}{gwSnpScreenResult-class}{cwSnpScreenResult.Rdash.class}
\aliasA{multiGwSnpScreenResult-class}{gwSnpScreenResult-class}{multiGwSnpScreenResult.Rdash.class}
\keyword{classes}{gwSnpScreenResult-class}
\begin{Description}\relax
Class "gwSnpScreenResult" -- container for GGtools gwSnpScreen
method outputs and allied objects
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("gwSnpScreenResult", ...)}.
These will be primarily lists of inference tables (snps are rows,
columns are statistics and p-values).  Additional slots
manage analysis metadata.

gwSnpScreenResult is intended for genome-wide analysis of expression
for a single gene.

cwSnpScreenResult is intended for the restriction to a single
chromosome.

multiGwSnpScreenResult is intended for analyses with multiple genes.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{.Data}:] Object of class \code{"list"} containing
inference tables (snps are rows, columns are statistics and
p-values) 
\item[\code{gene}:] Object of class \code{"character"} typically
the HUGO symbol of the gene analyzed 
\item[\code{psid}:] Object of class \code{"character"} the
feature identifier of the associated microarray 
\item[\code{annotation}:] Object of class \code{"character"} vector
of relevant annotation package identifier names 
\item[\code{snpLocPackage}:] Object of class \code{"character"} name
of package holding the netCDF store of SNP locations 
\item[\code{snpLocExtRef}:] Object of class \code{"character"} name
of object in snpLocPackage pointing to the external store (SQLite) 
\item[\code{activeSnpInds}:] Object of class \code{"numeric"} vector
telling which SNPs (relative to the referenced netCDF locations store)
were used

}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{list}{list.Rdash.class}"}, from data part.
Class \code{"\LinkA{vector}{vector.Rdash.class}"}, by class "list", distance 2.
Class \code{"\LinkA{AssayData}{AssayData}"}, by class "list", distance 2.
\end{Section}
\begin{Section}{Methods}
No methods defined with class "gwSnpScreenResult" in the signature in
class GGBase.  See GGtools gwSnpScreen documentation.
\end{Section}
\begin{Author}\relax
VJ Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
showClass("gwSnpScreenResult")
showClass("cwSnpScreenResult")
\end{ExampleCode}
\end{Examples}

