R/interestingGroups-methods.R

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

#' @name interestingGroups
#' @inherit AcidGenerics::interestingGroups
#' @note Updated 2019-08-11.
#'
#' @inheritParams AcidRoxygen::params
#' @param ... Additional arguments.
#'
#' @examples
#' data(RangedSummarizedExperiment, package = "AcidTest")
#' rse <- RangedSummarizedExperiment
#'
#' ## SummarizedExperiment ====
#' intgroup <- interestingGroups(rse)
#' print(intgroup)
#' ## Assignment support.
#' interestingGroups(rse) <- intgroup[[1L]]
#' interestingGroups(rse)
NULL



## Updated 2019-07-22.
`interestingGroups,Annotated` <- # nolint
    function(object) {
        metadata(object)[["interestingGroups"]]
    }



## Updated 2019-07-22.
`interestingGroups<-,Annotated,character` <- # nolint
    function(object, value) {
        assert(areDisjointSets(value, "interestingGroups"))
        metadata(object)[["interestingGroups"]] <- value
        object
    }



## Note that we're always allowing `sampleName` to be slotted, even if that
## column isn't defined in `colData()`.
##
## Updated 2019-08-11.
`interestingGroups<-,SE,character` <- # nolint
    function(object, value) {
        assert(areDisjointSets(value, "interestingGroups"))
        setdiff <- setdiff(value, colnames(sampleData(object)))
        if (hasLength(setdiff)) {
            abort(sprintf(
                "Columns not defined in {.fun %s}: %s.",
                "sampleData",
                toInlineString(setdiff, n = 5L, class = "val")
            ))
        }
        metadata(object)[["interestingGroups"]] <- value
        object
    }



## Updated 2019-07-22.
`interestingGroups<-,Annotated,NULL` <- # nolint
    function(object, value) {
        metadata(object)[["interestingGroups"]] <- NULL
        object
    }



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



#' @rdname interestingGroups
#' @export
setReplaceMethod(
    f = "interestingGroups",
    signature = signature(
        object = "Annotated",
        value = "NULL"
    ),
    definition = `interestingGroups<-,Annotated,NULL`
)

#' @rdname interestingGroups
#' @export
setReplaceMethod(
    f = "interestingGroups",
    signature = signature(
        object = "Annotated",
        value = "character"
    ),
    definition = `interestingGroups<-,Annotated,character`
)

#' @rdname interestingGroups
#' @export
setReplaceMethod(
    f = "interestingGroups",
    signature = signature(
        object = "SummarizedExperiment",
        value = "character"
    ),
    definition = `interestingGroups<-,SE,character`
)