R/MuraroPancreasData.R

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

#' Obtain the Muraro pancreas data
#'
#' Obtain the human pancreas single-cell RNA-seq data from Muraro et al. (2016).
#'
#' @param ensembl Logical scalar indicating whether the output row names should contain Ensembl identifiers.
#' @param location Logical scalar indicating whether genomic coordinates should be returned.
#' @param legacy Logical scalar indicating whether to pull data from ExperimentHub.
#' By default, we use data from the gypsum backend.
#' 
#' @details
#' Row data contains fields for the symbol and chromosomal location of each gene.
#'
#' Column metadata is derived from the columns of the count matrix provided in GSE85241,
#' with additional cell type labels obtained from the authors (indirectly, via the Hemberg group).
#' Some cells have \code{NA} labels and were presumably removed prior to downstream analyses.
#'
#' Count data for ERCC spike-ins are stored in the \code{"ERCC"} entry of the \code{\link{altExps}}.
#'
#' If \code{ensembl=TRUE}, the gene symbols are converted to Ensembl IDs in the row names of the output object.
#' Rows with missing Ensembl IDs are discarded, and only the first occurrence of duplicated IDs is retained.
#'
#' If \code{location=TRUE}, the coordinates of the Ensembl gene models are stored in the \code{\link{rowRanges}} of the output.
#' Note that this is only performed if \code{ensembl=TRUE}.
#'
#' All data are downloaded from ExperimentHub and cached for local re-use.
#' Specific resources can be retrieved by searching for \code{scRNAseq/muraro-pancreas}.
#'
#' @return A \linkS4class{SingleCellExperiment} object with a single matrix of UMI counts.
#'
#' @author Aaron Lun,
#' using additional metadata obtained by Vladimir Kiselev.
#'
#' @references
#' Muraro MJ et al. (2016). 
#' A single-cell transcriptome atlas of the human pancreas.
#' \emph{Cell Syst.} 3(4), 385-394.
#'
#' @examples
#' sce <- MuraroPancreasData()
#' 
#' @export
#' @importFrom S4Vectors DataFrame
#' @importFrom SummarizedExperiment rowData<-
#' @importFrom SingleCellExperiment splitAltExps
MuraroPancreasData <- function(ensembl=FALSE, location=TRUE, legacy=FALSE) {
    if (!legacy) {
        sce <- fetchDataset("muraro-pancreas-2016", "2023-12-19", realize.assays=TRUE)

    } else {
        version <- "2.0.0"
        sce <- .create_sce(file.path("muraro-pancreas", version), has.rowdata=FALSE) 

        symbol <- sub("__.*", "", rownames(sce))
        loc <- sub(".*__", "", rownames(sce))
        rowData(sce) <- DataFrame(symbol=symbol, chr=loc)

        status <- ifelse(grepl("^ERCC-[0-9]+", symbol), "ERCC", "endogenous")
        sce <- splitAltExps(sce, status, ref="endogenous")
    }

    .convert_to_ensembl(sce,
        symbols=rowData(sce)$symbol,
        species="Hs",
        ensembl=ensembl,
        location=location)
}