\HeaderA{masterSnps}{visualize a multiGwSnpScreenResult}{masterSnps}
\keyword{models}{masterSnps}
\begin{Description}\relax
visualize a multiGwSnpScreenResult
\end{Description}
\begin{Usage}
\begin{verbatim}
masterSnps(mgw, n = 50, auto = TRUE, orgdb = "org.Hs.eg.db", minl10 = 5, 
gstart = 0, gend = 3e+09,
genomesize = 3e+09, pcex = 1, pal = rainbow(20), numxax=FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mgw}] a multiGwSnpScreenResult, for example from
gwSnpTests with a GeneSet on lhs of formula 
\item[\code{n}] number of best snps to retain per gene
\item[\code{auto}] restrict attention to autosomes? 
\item[\code{orgdb}] an annotation library like org.Hs.eg.db 
\item[\code{minl10}] threshold of -log10 p above which we keep SNP for plotting
\item[\code{gstart}] position at which genome-wide SNP locations begin
\item[\code{gend}] position at which genome-wide SNP locations end
\item[\code{genomesize}] number of bases over which plotting will be conducted
(e.g., ylim=c(0, genomesize) ) 
\item[\code{pcex}] cex setting for pch of plot 
\item[\code{pal}] a palette to differentiate gene coloring 
\item[\code{numxax}] logical: if TRUE, x axis labels genomic coordinates,
otherwise chromosome 
\item[\code{...}] args passed to plot() 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
experimental display with snp location as ordinate and
gene location as abscissa -- point plotted if snp is
associated with gene at p smaller than the threshold specified
\end{Details}
\begin{Value}
a list with self-describing elements
\end{Value}
\begin{Author}\relax
VJ Carey \textless{}stvjc@channing.harvard.edu\textgreater{}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
if (require("GGdata")) {
 data(fheadFits)
 mm7 = masterSnps(fheadFits, minl10=7, pal=rainbow(10))
 }
\end{ExampleCode}
\end{Examples}

