\name{lociData-class}
\docType{class}
\alias{lociData}
\alias{lociData-class}
\alias{dim,lociData-method}
\alias{[,lociData-method}
\alias{[,lociData,ANY,ANY-method}
\alias{show,lociData-method}

\title{Class "lociData"}

\description{
  The \code{lociData} class is based on the
  \code{\link{lociData}} class defined in the
  `baySeq' package, but includes a `coordinates' slot giving the
  coordinates of genomic loci and a `locLikelihoods' slot which contains
  the estimated likelihoods that each annotated region is a locus in
  each replicate group and a coordinates structure giving the locations
  of the loci.
}

\section{Slots}{
  \describe{
    \item{\code{locLikelihoods}:}{Object of class \code{"matrix"}
  describing estimated likelihoods that each region defined in
  `coordinates' is a locus in each replicate group.}
    \item{\code{coordinates}:}{Object of class \code{"GRanges"} defining
  the coordinates of the genomic loci.}
    \item{\code{data}:}{Object of class \code{"matrix"} defining count
  data for each locus defined in `coordinates'}
    \item{\code{replicates}:}{Object of class \code{"factor"} defining
  the replicate structure of the data.}
    \item{\code{libsizes}:}{Object of class \code{"numeric"} describing
  the library size (scaling factor) for each sample.}
    \item{\code{groups}:}{Object of class \code{"list"} defing the group
  (model) structure of the data (see the
  \code{\link[baySeq:baySeq-package]{baySeq} package})}.
    \item{\code{annotation}:}{Object of class \code{"data.frame"} giving
  any additional annotation information for each locus.}
    \item{\code{priorType}:}{Object of class \code{"character"}
  describing the type of prior information available in slot \code{'priors'}.}
    \item{\code{priors}:}{Object of class \code{"list"} defing the prior
      parameter information. Calculated by
      the \link[baySeq:baySeq-package]{baySeq} package.}
    \item{\code{posteriors}:}{Object of class \code{"matrix"} giving the
  estimated posterior likelihoods for each replicate group. Calculated by
  the \link[baySeq:baySeq-package]{baySeq} package.}
    \item{\code{nullPosts}:}{Object of class \code{"numeric"} which, if
  calculated, defines the posterior likelihoods for the data having no
  true expression of any kind. Calculated by
  the \link[baySeq:baySeq-package]{baySeq} package.}
    \item{\code{estProps}:}{Object of class \code{"numeric"} giving the
  estimated proportion of tags belonnging to each group. Calculated by
  the \link[baySeq:baySeq-package]{baySeq} package.}
    \item{\code{seglens}:}{Object of class \code{"matrix"} defining the
  lengths of each segment containing the counts described in the
  \code{'data'} slot. May be initialised with a vector, or ignored altogether.}
  }
}

\section{Extends}{
Class \code{"\linkS4class{lociData}"}, directly.
}

\section{Details}{
The \code{seglens} slot describes, for each row of the \code{data}
object, the length of the segment that contains the number of counts
described by that row. For example, if we are looking at the number of
hits matching genes, the \code{seglens} object would consist of
transcript lengths. Exceptionally, we may want to use different segment
lengths for different samples and so the slot takes the form of a
matrix. If the matrix has only one column, it is duplicated for all
samples. Otherwise, it should have the same number of columns as the
'data' slot. If the slot is the empty matrix, then it is assumed that
all segments have the same length.
}

\section{Methods}{
  Methods `new', `dim', `[' and `show' have been defined for this class.
}

\author{Thomas J. Hardcastle}

\keyword{classes}