R/interestingGroups-methods.R

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

#' @name interestingGroups
#' @inherit AcidGenerics::interestingGroups
#' @note Updated 2021-03-15.
#'
#' @inheritParams AcidRoxygen::params
#' @param ... Additional arguments.
#'
#' @examples
#' data(deseq)
#'
#' ## DESeqAnalysis ====
#' intgroup <- interestingGroups(deseq)
#' print(intgroup)
#' ## Assignment support.
#' interestingGroups(deseq) <- intgroup
#' interestingGroups(deseq)
NULL



## Updated 2020-08-04.
`interestingGroups,DESeqAnalysis` <- # nolint
    function(object) {
        dds <- as(object, "DESeqDataSet")
        interestingGroups(dds)
    }



## Updated 2020-08-04.
`interestingGroups<-,DESeqAnalysis,character` <- # nolint
    function(object, value) {
        data <- slot(object, "data")
        transform <- slot(object, "transform")
        interestingGroups(data) <- value
        interestingGroups(transform) <- value
        slot(object, "data") <- data
        slot(object, "transform") <- transform
        object
    }



`interestingGroups<-,DESeqAnalysis,NULL` <- # nolint
    `interestingGroups<-,DESeqAnalysis,character`



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



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

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