\name{deepSNV-methods}
\alias{deepSNV-methods}
\alias{deepSNV}
\title{Test two matched deep sequencing experiments for low-frequency SNVs.}
\description{Test two matched deep sequencing experiments for low-frequency SNVs.}
\details{\code{deepSNV-methods}: This generic function can handle different types of inputs for the test and control experiments. It either reads from two .bam files,
uses two matrices of nucleotide counts, or re-evaluates the test results from a \code{\link{deepSNV-class}} object. The actual test is a
likelihood ratio test of a (beta-)binomial model for the individual nucleotide counts on each position under the hypothesis that both experiments share the same parameter,
and the alternative that the parameters differ. Because the difference in degrees of freedom is 1, the test statistic \eqn{D = -2 \log \max{L_0}/\max{L_1}}
is asymptotically distributed as \eqn{\chi_1^2}. The statistic may be tuned by a nucleotide specific Dirichlet prior that is learned across all genomic sites, 
see \code{\link{estimateDirichlet}}. If the model is beta-binomial, a global dispersion parameter is used for all sites. It can be learned with \code{\link{estimateDispersion}}.

}
\value{\code{deepSNV-methods}: A \code{\linkS4class{deepSNV}} object

}
\author{gemoritz}
\arguments{\item{test}{The test experiment. Either a .bam file, or a matrix with nucleotide counts, or  a \code{\link{deepSNV-class}} object.}
\item{control}{The control experiment. Must be of the same type as test, or missing if test is  a \code{\link{deepSNV-class}} object.}
\item{alternative}{The alternative to be tested. One of greater, less, or two.sided.}
\item{model}{Which model to use. Either "bin", or "betabin". Default "bin".}
\item{dirichlet.prior}{A base-sepecific Dirichlet prior specified as a matrix. Default NULL.}
\item{pseudo.count}{If dirichlet.prior=NULL, a pseudocount can be used to define a flat prior.}
\item{over.dispersion}{A numeric factor for the over.dispersion, if the model is beta-binomial. Default 100.}
\item{combine.method}{The method to combine p-values. One of "fisher" (default), "max", or "average". See \code{\link{p.combine}} for details.}
\item{regions}{The regions to be parsed if test and control are .bam files. Either a \code{\link{data.frame}} with columns "chr" (chromosome), 
"start", "stop", or a \code{\link{GRanges}} object. If multiple regions are specified, the appropriate slots of the returned object are concatenated by row.}
\item{q}{The quality arguement  passed to \code{\link{bam2R}} if the experiments are .bam files.}
\item{s}{The strand argument  passed to \code{\link{bam2R}} if the experiments are .bam files.}
\item{head.clip}{The head.clip argument  passed to \code{\link{bam2R}} if the experiments are .bam files.}
\item{...}{Additional arguments.}
}
\examples{## Short example with 2 SNVs at frequency ~10%
regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140)
ex <- deepSNV(test = system.file("extdata", "test.bam", package="deepSNV"), control = system.file("extdata", "control.bam", package="deepSNV"), regions=regions, q=10)
show(ex)   # show method
plot(ex)   # scatter plot
summary(ex)   # summary with significant SNVs
ex[1:3,]   # subsetting the first three genomic positions
tail(test(ex, total=TRUE))   # retrieve the test counts on both strands
tail(control(ex, total=TRUE))

## Not run: Full example with ~ 100 SNVs. Requires an internet connection, but try yourself.
# regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585)
# HIVmix <- deepSNV(test = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", control = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", regions=regions, q=10)
data(HIVmix) # attach data instead..
show(HIVmix)
plot(HIVmix)
head(summary(HIVmix))}
\alias{deepSNV,matrix,matrix-method}
\alias{deepSNV}
\usage{\S4method{deepSNV}{matrix,matrix}(test, control, alternative=c("greater", "less", "two.sided"),
    dirichlet.prior, pseudo.count=1, combine.method=c("fisher", "max",
    "average"), over.dispersion=100, model=c("bin", "betabin"), ...)
\S4method{deepSNV}{deepSNV,missing}(test, control, ...)
\S4method{deepSNV}{character,character}(test, control, regions, q=25, s=2, head.clip=0, ...)
\S4method{deepSNV}{matrix,character}(test, control, regions, q=25, s=2, ...)
\S4method{deepSNV}{character,matrix}(test, control, regions, q=25, s=2, ...)
}
\alias{deepSNV,deepSNV,missing-method}
\alias{deepSNV}
\alias{deepSNV,character,character-method}
\alias{deepSNV}
\alias{deepSNV,matrix,character-method}
\alias{deepSNV}
\alias{deepSNV,character,matrix-method}
\alias{deepSNV}