% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/RizzardiHickeyBrainData.R
\name{RizzardiHickeyBrain}
\alias{RizzardiHickeyBrain}
\title{Obtain the Rizzardi/Hickey brain data}
\usage{
RizzardiHickeyBrain(
  context = c("CpG", "CpA", "CpT"),
  strand = c("*", "+", "-"),
  HDF5Array = TRUE
)
}
\arguments{
\item{context}{A string specifying the context of the methylation loci to be obtained.}

\item{strand}{A string specifying the strand of the methylation loci to be obtained.}

\item{HDF5Array}{Logical scalar indicating whether the assays should be returned as \linkS4class{HDF5Array} objects or as ordinary \link{matrix} objects.}
}
\value{
A \linkS4class{SummarizedExperiment} object with assays containing a matrix of methylated read counts (\code{M}) and a matrix of total read counts (\code{Cov}).
}
\description{
Obtain the human brain nuclei whole genome bisulfite sequencing (WGBS) data from Rizzardi, Hickey, et al. (2019).
}
\details{
The data consists of WGBS methylation profiles of neuronal, non-neuronal, and unsorted  nuclei populations from four different regions of the human brain, with \eqn{n = 4 - 9} biological replicates for each condition (i.e. the combination of nuclei population and brain region).

Column metadata include:
\itemize{
  \item \code{donor} The donor ID
  \item \code{neun} The nuclei population as determined using fluorescence-activated nuclear sorting based on the neuronal marker NeuN
  \itemize{
    \item \code{"pos"} Neuronal (NeuN+) nuclei
    \item \code{"neg"} Non-neuronal (NeuN-) nuclei
    \item \code{"unsorted"} Unsorted nuclei (i.e. including both neuronal (Neun+) and non-neuronal (NeuN-) nuclei in unknown proportions).
  }
  \item \code{tissue} The brain region
  \itemize{
    \item \code{"BA9"} Brodmann area 9 (part of the frontal cortex)
    \item \code{"BA24"} Brodmann area 9 (part of the anterior cingulate)
    \item \code{"HC"} Hippocampus
    \item \code{"NAcc"} Nucleus accumbens
  }
}
The majority of donors were matched between sorted and unsorted populations, but not all.

Separate datasets are provided for five sets of methylation loci:
\itemize{
  \item CpGs (\code{context = "CpG"}) aggregated across strands (and thus unstranded,  \code{strand = "*"})
  \item CpAs (\code{context = "CpA"}) on the forward strand (\code{strand = "+"})
  \item CpAs (\code{context = "CpA"}) on the reverse strand (\code{strand = "-"})
  \item CpTs (\code{context = "CpT"}) on the forward strand (\code{strand = "+"})
  \item CpTs (\code{context = "CpT"}) on the reverse strand (\code{strand = "-"})
}
Data from the unsorted nuclei are not available for the CpA or CpT datasets.

If \code{HDF5Array = TRUE} then the each assay is returned as a \linkS4class{HDF5Array} object.
Each \linkS4class{HDF5Array} occupies approximately 2 KB in memory.
If \code{HDF5Array = FALSE} then the each assay is returned as an ordinary \link{matrix} objects.
Each matrix occupies approximately \eqn{6 - 33} GiB in memory (smaller for CpG, larger for CpA and CpT).

All data are downloaded from ExperimentHub and cached for local re-use.
Specific resources can be retrieved by searching for \code{MethylSeqdata/rizzardi_hickey_brain}.
}
\examples{
se <- RizzardiHickeyBrain()

}
\references{
Rizzardi, Hickey, et al. (2019)
Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.
\emph{Nature neuroscience} 22(2), 307-316.
\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348048/}
}
\author{
Peter Hickey
}
