R/lfcThreshold-methods.R

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

#' @name lfcThreshold
#' @inherit AcidGenerics::lfcThreshold
#' @note Updated 2021-03-12.
#'
#' @details
#' Assumes `0` by default if unset.
#'
#' @param ... Additional arguments.
#'
#' @examples
#' data(deseq)
#'
#' ## DESeqAnalysis ====
#' lfcThreshold(deseq) <- 0.2
#' lfcThreshold(deseq)
NULL



## Updated 2021-03-12.
`lfcThreshold,DESeqAnalysis` <- # nolint
    function(object) {
        x <- metadata(object)[["lfcThreshold"]]
        if (is.null(x)) {
            resList <- DESeqResultsList(object, quiet = TRUE)
            x <- lfcThreshold(resList)
        }
        assert(isNumber(x), isNonNegative(x))
        x
    }



## Updated 2021-03-12.
`lfcThreshold,DESeqAnalysisList` <- # nolint
    function(object) {
        assert(hasLength(object))
        x <- metadata(object)[["lfcThreshold"]]
        if (is.null(x)) {
            x <- lfcThreshold(object[[1L]])
        }
        assert(isNumber(x), isNonNegative(x))
        x
    }



## Updated 2021-03-03.
`lfcThreshold,DESeqResults` <- # nolint
    function(object) {
        x <- metadata(object)[["lfcThreshold"]]
        if (is.null(x)) {
            x <- 0L
        }
        assert(isNumber(x), isNonNegative(x))
        x
    }



## Updated 2021-03-12.
`lfcThreshold,DESeqResultsList` <- # nolint
    function(object) {
        assert(hasLength(object))
        x <- metadata(object)[["lfcThreshold"]]
        if (is.null(x)) {
            x <- lfcThreshold(object[[1L]])
        }
        assert(isNumber(x), isNonNegative(x))
        x
    }



## Updated 2021-03-03.
`lfcThreshold<-,DESeqAnalysis,numeric` <- # nolint
    function(object, value) {
        assert(isScalar(value), isNonNegative(value))
        metadata(object)[["lfcThreshold"]] <- value
        object
    }



## Updated 2020-08-04.
`lfcThreshold<-,DESeqAnalysis,NULL` <- # nolint
    function(object, value) {
        metadata(object)[["lfcThreshold"]] <- value
        object
    }



## Updated 2021-03-13.
`lfcThreshold<-,DESeqAnalysisList,numeric` <- # nolint
    `lfcThreshold<-,DESeqAnalysis,numeric`



## Updated 2021-03-13.
`lfcThreshold<-,DESeqAnalysisList,NULL` <- # nolint
    `lfcThreshold<-,DESeqAnalysis,NULL`



## Updated 2021-03-12.
`lfcThreshold<-,DESeqResults,numeric` <- # nolint
    `lfcThreshold<-,DESeqAnalysis,numeric`



## Updated 2021-03-13.
`lfcThreshold<-,DESeqResultsList,numeric` <- # nolint
    `lfcThreshold<-,DESeqResults,numeric`



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

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

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

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



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

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

#' @rdname lfcThreshold
#' @export
setReplaceMethod(
    f = "lfcThreshold",
    signature = signature(
        object = "DESeqAnalysisList",
        value = "numeric"
    ),
    definition = `lfcThreshold<-,DESeqAnalysisList,numeric`
)

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

#' @rdname lfcThreshold
#' @export
setReplaceMethod(
    f = "lfcThreshold",
    signature = signature(
        object = "DESeqResults",
        value = "numeric"
    ),
    definition = `lfcThreshold<-,DESeqResults,numeric`
)

#' @rdname lfcThreshold
#' @export
setReplaceMethod(
    f = "lfcThreshold",
    signature = signature(
        object = "DESeqResultsList",
        value = "numeric"
    ),
    definition = `lfcThreshold<-,DESeqResultsList,numeric`
)