\HeaderA{gwSnpScreen-methods}{genome-wide test for association between SNP and phenotype}{gwSnpScreen.Rdash.methods}
\aliasA{cnumOrMissing-class}{gwSnpScreen-methods}{cnumOrMissing.Rdash.class}
\aliasA{cwSnpScreen}{gwSnpScreen-methods}{cwSnpScreen}
\aliasA{gwSnpScreen}{gwSnpScreen-methods}{gwSnpScreen}
\aliasA{gwSnpScreen,GeneSet,smlSet,cnumOrMissing-method}{gwSnpScreen-methods}{gwSnpScreen,GeneSet,smlSet,cnumOrMissing.Rdash.method}
\aliasA{gwSnpScreen,genesym,smlSet,cnumOrMissing-method}{gwSnpScreen-methods}{gwSnpScreen,genesym,smlSet,cnumOrMissing.Rdash.method}
\aliasA{gwSnpScreen,genesym,smlSet-method}{gwSnpScreen-methods}{gwSnpScreen,genesym,smlSet.Rdash.method}
\keyword{methods}{gwSnpScreen-methods}
\keyword{models}{gwSnpScreen-methods}
\begin{Description}\relax
genome-wide test for association between SNP and phenotype
\end{Description}
\begin{Section}{Methods}
\describe{
\item[sym = "genesym", sms = "smlSet", cnum="cnumOrMissing"] \code{sym} is an instance
of \code{genesym} class (typically just a wrapped character string
giving a SYMBOL value for the expression annotation package in use, or
a GeneSet instance, see below);
\code{sms} is an integrative instance of \code{smlSet} containing
snp.matrix genotype data in a list and coordinated expression data.
Restriction of analysis to specific chromosomes can be accomplished by
passing an instance of \code{chrnum} as the third argument.

The \code{gwSnpScreen} computes the snp.rhs.tests from snpMatrix
for all snp against the specified expression phenotype.

If \code{sym} is an instance of the GSEABase GeneSet class,
a list of gwSnpScreenResults is packaged in a multiGwSnpScreenResult
instance.
}
\end{Section}
\begin{Examples}
\begin{ExampleCode}
data(hmceuB36.2021)
objects("package:GGBase")
g1 = gwSnpScreen( genesym("CPNE1"), hmceuB36.2021, chrnum(20) )
g1
plot(g1)
\end{ExampleCode}
\end{Examples}

