R/dsa.R

In PeteHaitch/DRMatrix: Compressed In-Memory Representation of 3-Dimensional Arrays That Contain Many Duplicate Slices

#' A \linkS4class{DSArray} object storing the counts of methylation patterns at
#' 4-tuples.
#'
#' A dataset containing counts of methylation patterns at 1,000,000 randomly
#' sampled CpG 4-tuples from 17 samples. Whilst these data are extracted from
#' real biological experiments, they are for illustrative purposes only and are
#' fairly useless without the associated genomic co-ordinates and other
#' metadata.
#'
#' The \linkS4class{DSArray} representation of the data use 70 Mb of memory
#' compared to 1 Gb for the \link[base]{array} representation.
#'
#' @format A \linkS4class{DSArray} object with 1,000,000 rows (tuples),
#' 17 columns (samples), and 16 slices (possible methylation patterns):
#' \describe{
#'  \item{Rows}{rows have been deidentified by removing the genomic
#'    co-ordinates}
#'  \item{Columns}{sample names. Please consult the original publications for
#'    sample descriptions}
#'  \item{Slices}{The type of methylation pattern, e.g., \code{MMMM} means
#'    methylated at all 4 CpGs in the 4-tuple}
#' }
#' @source Data originally published in:
#' \itemize{
#'  \item Lister, R. et al. Human DNA methylomes at base resolution show
#'    widespread epigenomic differences. Nature 462,315-322 (2009)
#'  \item Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in
#'    human induced pluripotent stem cells. Nature 471, 68-73 (2011)
#' }
#' Data re-analysed by Peter Hickey using \code{methtuple}
#' (\url{https://github.com/PeteHaitch/methtuple}) to extract the methylation
#' patterns at 4-tuples.
"dsa"