R/geneNames-methods.R

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

#' @name geneNames
#' @inherit AcidGenerics::geneNames
#' @note Updated 2019-07-28.
#'
#' @inheritParams AcidRoxygen::params
#' @param ... Additional arguments.
#'
#' @examples
#' data(RangedSummarizedExperiment, package = "AcidTest")
#' rse <- RangedSummarizedExperiment
#'
#' ## SummarizedExperiment ====
#' head(geneNames(rse))
NULL



## Updated 2019-07-22.
`geneNames,Vector` <- # nolint
    function(object) {
        GeneToSymbol(object, format = "makeUnique")[["geneName"]]
    }



## Updated 2019-07-22.
`geneNames,GRanges` <- # nolint
    `geneNames,Vector`



## Updated 2019-07-22.
`geneNames,SE` <- # nolint
    `geneNames,Vector`



#' @rdname geneNames
#' @export
setMethod(
    f = "geneNames",
    signature = signature(object = "GRanges"),
    definition = `geneNames,GRanges`
)

#' @rdname geneNames
#' @export
setMethod(
    f = "geneNames",
    signature = signature(object = "SummarizedExperiment"),
    definition = `geneNames,SE`
)