Adding the MethylCounts-class man page

Author: kasperdanielhansen

man/MethylCounts-class.Rd

@@ -0,0 +1,122 @@
+\name{MethylCounts-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{MethylCounts-class}
+\alias{show,MethylCounts-method}
+\alias{getMethylCounts}
+\alias{MethylCounts}
+\title{Class MethylCounts}
+\description{
+  A class for representing whole-genome or capture sequencing
+  methylation data.
+}
+\section{Objects from the Class}{
+  An object from the class links together several pieces of information.
+  (1) genomic locations stored as a \code{GRanges} object, a location by
+  samples matrix of M values, a location by samples matrix of Cov
+  (coverage) values, a location by samples matrix of Filtered (ambiguous
+  modification status) values, and phenodata information.In addition,
+  there are slots for representing smoothed data. This class is an
+  extension of \link[SummarizedExperiment]{RangedSummarizedExperiment}
+  from the \pkg{SummarizedExperiment} package.
+}
+\section{Slots}{
+  In addition to the slots from \code{RangedSummarizedExperiment} we have
+  \describe{
+    \item{\code{parameters}:}{Object of class \code{list}.  A list of
+      parameters representing for example how the data was smoothed.}
+  }
+}
+\section{Methods}{
+  \describe{
+    \item{show}{The show method.}
+  }
+}
+\usage{
+  MethylCounts(M = NULL, U = NULL, H = NULL, D = NULL, 
+               gr = NULL, pos = NULL, chr = NULL,
+               colData = NULL, sampleNames = NULL,
+               parameters = NULL, rmZeroCov = FALSE)
+
+  getMethylCounts(MethylCounts,
+                  type = c("M", "U", "H", "D", "Cov", "gr", "parameters"),
+                  withDimnames = TRUE)
+}
+\arguments{
+  \item{M}{A matrix-like object of M values (see 'Details' below).}
+  \item{U}{A matrix-like object of U values (see 'Details' below).}
+  \item{H}{An optional matrix-like object of H values (see 'Details'
+    below).}
+  \item{D}{An optional matrix-like object of D values (see 'Details' below).}
+  \item{gr}{An object of type \code{\link[GenomicRanges]{GRanges}}.}
+  \item{pos}{A vector of locations.}
+  \item{chr}{A vector of chromosomes.}
+  \item{colData}{Typically a \code{DataFrame} with sample
+    coveriates. See the documentation for \code{SummarizedExperiment}.}
+  \item{sampleNames}{A character vector of sample names.}
+  \item{parameters}{A list of parameters, for record-keeping.}
+  \item{rmZeroCov}{\code{logical(1)}. Remove loci with zero coverage}
+  \item{MethylCounts}{An object of class \code{MethylCounts}.}
+  \item{type}{What should be extracted from the object?}
+  \item{withDimnames}{\code{logical(1)}. Should dimnames be added to the
+                  output when relevent?} 
+}
+\section{Details}{
+  The \code{M}, \code{U}, \code{H}, and \code{D} matrix-like objects will be
+  coerced to \code{\link[DelayedArray]{DelayedMatrix}} objects; see
+  \code{\link[DelayedArray]{DelayedMatrix}} in the \pkg{DelayedArray}
+  package for the full list of supported matrix-like objects. We
+  recommend using \link[base]{matrix} objects for in-memory storage of
+  data and \code{\link[HDF5Array]{HDF5Matrix}} for on-disk storage of
+  data. These objects should have the same dimension and be integer-values.
+
+  \code{M}, \code{U} are required methylation and 'unmethylation'
+  values. \code{H} is optional hydroxymethylation values. \code{D}
+  represents addition coverage for a loci, but where the data supports
+  neither M, U nor H.
+  
+  The argument \code{rmZeroCov} may be useful in order to reduce the
+  size of the return object be removing methylation loci with zero
+  coverage.
+
+  \code{pos} and \code{chr} can be supplied instead of \code{gr}.
+}
+\section{Utilities}{
+  This class extends
+  \link[SummarizedExperiment]{RangedSummarizedExperiment}
+  from the \pkg{SummarizedExperiment} package and therefore
+  inherits a number of useful \code{GRanges} methods that operate on the
+  \code{rowRanges} slot, used for accessing and setting the genomic locations
+  and also do \code{subsetByOverlaps}.
+
+  There are a number of almost methods-like functions for operating on
+  objects of class \code{MethylCounts}, including
+  \code{getMethylCounts}. They are detailed below.
+
+  \describe{
+    \item{\code{getMethylCounts(MethylCounts, type, withDimnames)}}{
+      A general accessor: is used to obtain a specific slot of an object of
+      class \code{MethylCounts}.}
+  }
+}
+\author{
+  Kasper Daniel Hansen \email{khansen@jhsph.edu}
+}
+\seealso{
+  The package vignette.
+  \code{\link[SummarizedExperiment]{RangedSummarizedExperiment}}
+  (in the \pkg{SummarizedExperiment} package) for the underlying class.
+}
+\examples{
+M <- matrix(1:9, 3,3)
+colnames(M) <- c("A1", "A2", "A3")
+MCtest <- MethylCounts(pos = 1:3,
+                       chr = c("chr1", "chr2", "chr1"),
+                       M = M, U = M + 2)
+
+#-------------------------------------------------------------------------------
+# An example using a HDF5-backed MethylCounts object
+#
+hdf5_NCtest <- realize(MCtest, "HDF5Array")
+}
+\keyword{classes}