R/KnownMarkers.R

In acidgenomics/AcidGenerics: Acid Genomics Generics

#' Known cell markers
#'
#' @export
#'
#' @description
#' Objects must contain Ensembl gene identifiers in the `geneId` column. We
#' must avoid any matching operations based on the gene names, since these
#' change often and can mismatch easily.
#'
#' @inheritParams AcidRoxygen::params
#'
#' @param markers
#' Object containing cell markers from differential expression analysis.
#' (e.g. `SeuratMarkers`).
#'
#' @param known
#' Object containing known cell-type-specific marker genes
#' (e.g. `CellTypeMarkers`).
#'
#' @return `KnownMarkers`.
#'
#' @examples
#' showMethods("KnownMarkers")
setGeneric(
    name = "KnownMarkers",
    def = function(markers, known, ...) {
        standardGeneric("KnownMarkers")
    }
)