R/FletcherOlfactoryData.R

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

#' Obtain the Fletcher Olfactory data
#'
#' Obtain the mouse olfactory epithelial HBC stem cell differentiation dataset
#' from Fletcher et al. (2017).
#'
#' @param filtered Logical scalar indicating whether to filter out cells that
#'   were not used by the authors.
#' @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.
#' @details Column metadata is scraped from GEO, using both the author-supplied
#' \dQuote{phenoData} per-cell annotations and the author-supplied
#' \dQuote{protocolData} per-cell annotations. The former includes information
#' about the animals and the instruments, while the latter contains QC
#' statistics.
#' 
#' We also included the clustering results from the authors' analysis.
#'
#' If \code{filtered=TRUE}, only the cells used by the authors in their cluster
#' analysis are returned. Otherwise, the cells not used by the authors will have
#' \code{NA} in the clustering columns of the \code{\link{colData}}.
#'
#' 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.
#' 
#' All data are downloaded from ExperimentHub and cached for local re-use.
#' Specific resources can be retrieved by searching for
#' \code{scRNAseq/fletcher-olfactory}.
#'
#' @return A \linkS4class{SingleCellExperiment} object with a single matrix of
#'   read counts.
#'
#' @author Davide Risso
#'
#' @references
#' Fletcher et al. (2017). Deconstructing Olfactory Stem
#' Cell Trajectories at Single-Cell Resolution. \emph{Cell Stem Cell} 20(6):
#' 817–30.
#'
#' @examples
#' sce <- FletcherOlfactoryData()
#' 
#' @export
#' @importFrom SingleCellExperiment splitAltExps altExp altExp<-
#' @importFrom SummarizedExperiment rowData rowData<-
FletcherOlfactoryData <- function(filtered=TRUE, ensembl=FALSE, location=TRUE) {
    version <- "2.6.0"

    sce <- .create_sce(file.path("fletcher-olfactory", version), has.rowdata=TRUE)

    if (filtered) {
        sce <- sce[,!is.na(sce$cluster_id)]
    }

    type <- ifelse(rowData(sce)$Transcript_Type == "brainProjectControl", 
                   "control", "endogenous")
    sce <- splitAltExps(sce, type, ref="endogenous")
    
    .convert_to_ensembl(sce, 
                        symbols=rownames(sce), 
                        species="Mm",
                        ensembl=ensembl,
                        location=location)
}