\HeaderA{gwSnpTests}{methods for iterating association tests (expression vs SNP)
across genomes or chromosomes}{gwSnpTests}
\aliasA{gwSnpScreen}{gwSnpTests}{gwSnpScreen}
\aliasA{gwSnpTests,formula,smlSet,cnumOrMissing-method}{gwSnpTests}{gwSnpTests,formula,smlSet,cnumOrMissing.Rdash.method}
\aliasA{gwSnpTests,formula,smlSet,snpdepth-method}{gwSnpTests}{gwSnpTests,formula,smlSet,snpdepth.Rdash.method}
\aliasA{residTests}{gwSnpTests}{residTests}
\aliasA{residTests,cwSnpScreenResult,smlSet,formula,missing-method}{gwSnpTests}{residTests,cwSnpScreenResult,smlSet,formula,missing.Rdash.method}
\keyword{models}{gwSnpTests}
\begin{Description}\relax
methods for iterating association tests (expression vs SNP)
across genomes or chromosomes
\end{Description}
\begin{Usage}
\begin{verbatim}
gwSnpTests(sym, sms, cnum, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{sym}] genesym, probeId, or formula instance
\item[\code{sms}] smlSet instance
\item[\code{cnum}] chrnum instance or missing
\item[\code{...}] \dots
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
invokes snpMatrix test procedures as appropriate

gwSnpScreen is deprecated and simply throws a message indicating this.
\end{Details}
\begin{Value}
gwSnpScreenResult or cwSnpScreenResult instance
\end{Value}
\begin{Author}\relax
Vince Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
# condense to founders only
hmFou = hmceuB36.2021[, which(hmceuB36.2021$isFounder)]
# show basic formula fit
f1 = gwSnpTests(genesym("CPNE1")~male, hmFou, chrnum(20))
f1
plot(f1)
# show how to avoid adjusted fit
f1b = gwSnpTests(genesym("CPNE1")~1-1, hmFou, chrnum(20))
# show gene set modeling on chromosome
library(GSEABase)
gs1 = GeneSet(c("CPNE1", "ADA"))
geneIdType(gs1) = SymbolIdentifier()
f2 = gwSnpTests(gs1~male, hmFou, chrnum(20))
f2
names(f2)
plot(f2[["ADA"]])
# show 'smlSet-wide' fit
f3 = gwSnpTests(gs1~male, hmFou)
f3
\end{ExampleCode}
\end{Examples}

