\name{plotSNPs}
\alias{plotSNPs}
\alias{plotSamples}

\title{
Make M vs S plot for SNPs or samples.
}

\description{
These functions plot the M-values (log-ratios) versus S-values (average intensities)
for given SNP/(s) or sample/(s) or beanplots for M-values from different samples.
}

\usage{
plotSNPs(cnSet, row=1, offset=0, xlim=c(9,16), ylim=c(-5,5), verbose=FALSE)
plotSamples(cnSet, col=1, offset=0, xlim=c(9,16), ylim=c(-5,5), verbose=FALSE, sample=100000, seed=1, type="smoothScatter")
}

\arguments{
\item{cnSet}{An object of class \code{CNSet}}
\item{row}{scalar/vector of SNP indexes to plot}
\item{col}{scalar/vector of sample indexes to plot}
\item{offset}{numeric, offset to add to intensities in \code{cnSet}
before log2-transforming to make log-ratios or average log-intensities}
\item{xlim}{the x limits of the plot}
\item{ylim}{the y limits of the plot}
\item{verbose}{'logical.'  Whether to print descriptive messages during processing}
\item{sample}{integer indicating the number of SNPs to sample for the plot}
\item{seed}{integer seed for the random number generator to sample the SNPs}
\item{type}{character vector specifying the type of sample plot (either 'smoothScatter' or 'beanplot')}
}

\details{
The \code{plotSNPs} and \code{plotSamples} functions plot the M and S
values derived from the \code{cnSet} object.
}

\value{
One or more M vs S plot for \code{plotSNPs} for a given SNP(/s)
or either a smoothed scatter plot of M vs S or a beanplot of the M-values
for a selected sample(/s) for \code{plotSamples}.
}

\author{
Matt Ritchie and Cynthia Liu
}

\seealso{
\keyword{hplot}