\name{estimateDispersion-methods}
\alias{estimateDispersion-methods}
\alias{estimateDispersion}
\title{Estimate the Dispersion factor in a beta-binomial model.}
\description{Estimate the Dispersion factor in a beta-binomial model.}
\details{\code{estimateDispersion-methods}: This function estimates the dispersion factor in a beta-binomial model of the nucleotide counts. This model assumes that the count for nucleotide j at position i is
distributed after a beta-binomial \eqn{X_{i,j}\sim \mathrm{BB}(n_i; \alpha, \beta_{ij})}{X_ib ~ BB(n_i; alpha, beta_ij)}, where \eqn{n_i}{n_i} is the coverage.
The base and nucleotide specific parameter \eqn{\beta_{ij}}{beta_ij} is estimated from the local mean by the method-of-moments estimate, \eqn{\alpha}{alpha} is a shared
overdispersion parameter. It is estimated via a numerical optimization of the likelihood under the null-hypothesis.

}
\value{\code{estimateDispersion-methods}: A \code{\link{deepSNV-class}} object if the input was a deepSNV object. Otherwise the loglikelihood and the estimated parameter.

}
\author{gemoritz}
\arguments{\item{test}{Either a deepSNV object, or a matrix with the test counts.}
\item{control}{Missing if test is a deepSNV object, otherwise missing.}
\item{alternative}{The alternative to be tested. One of "greater", "less", "two-sided" (default). If test is a deepSNV object, automatically taken from the corresponding slot
if unspecified.}
\item{interval}{The interval to be screened for the overdispersion factor. Default (0,1000).}
}
\examples{data("RCC", package="deepSNV")
plot(RCC)
summary(RCC)[,1:6]
RCC.bb = estimateDispersion(RCC, alternative = "two.sided")
summary(RCC.bb)}
\alias{estimateDispersion,deepSNV,missing-method}
\alias{estimateDispersion}
\usage{\S4method{estimateDispersion}{deepSNV,missing}(test, control, alternative, interval=c(0, 1000))
\S4method{estimateDispersion}{matrix,matrix}(test, control, alternative, interval=c(0, 1000))
}
\alias{estimateDispersion,matrix,matrix-method}
\alias{estimateDispersion}