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resultsNames-methods.R
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resultsNames-methods.R
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#' @name resultsNames
#' @inherit AcidGenerics::resultsNames
#' @note Updated 2021-03-15.
#'
#' @inheritParams AcidRoxygen::params
#' @inheritParams params
#' @param ... Additional arguments.
#'
#' @examples
#' data(deseq)
#'
#' ## DESeqAnalysis ====
#' resultsNames(deseq)
NULL
## Updated 2021-03-15.
`resultsNames,DESeqAnalysis` <- # nolint
function(object) {
resList <- DESeqResultsList(object, quiet = TRUE)
names(resList)
}
## Updated 2021-03-15.
`resultsNames,DESeqAnalysisList` <- # nolint
`resultsNames,DESeqAnalysis`
## Updated 2019-07-23.
`resultsNames,DESeqDataSet` <- # nolint
function(object) {
DESeq2::resultsNames(object)
}
## Updated 2021-03-15.
`resultsNames,DESeqResultsList` <- # nolint
function(object) {
names(object)
}
## Updated 2023-12-18.
`resultsNames<-,DESeqAnalysis,character` <- # nolint
function(object, value) {
names(object@results) <- value
if (!is.null(object@lfcShrink)) {
names(object@lfcShrink) <- value
}
object
}
## Updated 2021-03-15.
`resultsNames<-,DESeqResultsList,character` <- # nolint
function(object, value) {
names(object) <- value
object
}
#' @rdname resultsNames
#' @export
setMethod(
f = "resultsNames",
signature = signature(object = "DESeqAnalysis"),
definition = `resultsNames,DESeqAnalysis`
)
#' @rdname resultsNames
#' @export
setMethod(
f = "resultsNames",
signature = signature(object = "DESeqAnalysisList"),
definition = `resultsNames,DESeqAnalysisList`
)
#' @rdname resultsNames
#' @export
setMethod(
f = "resultsNames",
signature = signature(object = "DESeqDataSet"),
definition = `resultsNames,DESeqDataSet`
)
#' @rdname resultsNames
#' @export
setMethod(
f = "resultsNames",
signature = signature(object = "DESeqResultsList"),
definition = `resultsNames,DESeqResultsList`
)
#' @rdname resultsNames
#' @export
setReplaceMethod(
f = "resultsNames",
signature = signature(
object = "DESeqAnalysis",
value = "character"
),
definition = `resultsNames<-,DESeqAnalysis,character`
)
#' @rdname resultsNames
#' @export
setReplaceMethod(
f = "resultsNames",
signature = signature(
object = "DESeqResultsList",
value = "character"
),
definition = `resultsNames<-,DESeqResultsList,character`
)