R/deprecated.R

In steinbaugh/S4Transformer: Coercion methods for biological data

## nocov start
## nolint start



#' @name deprecated
#' @inherit acidroxygen::deprecated description examples return seealso title
#' @inheritParams acidroxygen::params
#' @keywords internal
NULL



#' @name defunct
#' @inherit acidroxygen::defunct description examples return seealso title
#' @inheritParams acidroxygen::params
#' @keywords internal
NULL



## v0.2.4 ======================================================================
#' @rdname defunct
#' @name relevel
#' @importFrom stats relevel
#' @param ref Unsupported.
#' @usage relevel(x, ref, ...)
#' @export
NULL

#' @rdname defunct
#' @export
relevel.DataFrame <-  # nolint
    function(x, ref = NULL, ...) {
        .Defunct("droplevels")
    }

#' @rdname defunct
#' @export
relevel.Ranges <-  # nolint
    function(x, ref = NULL, ...) {
        .Defunct("droplevels")
    }

#' @rdname defunct
#' @export
relevel.SummarizedExperiment <-  # nolint
    function(x, ref = NULL, ...) {
        .Defunct("droplevels")
    }



## v0.2.7 ======================================================================
#' @rdname defunct
#' @name flatFiles
#' @importFrom bioverbs flatFiles
#' @export
NULL

`flatFiles,SummarizedExperiment` <-  # nolint
    function(object) {
        .Defunct("coerceToList")
    }

#' @rdname defunct
#' @export
setMethod(
    f = "flatFiles",
    signature = signature("SummarizedExperiment"),
    definition = `flatFiles,SummarizedExperiment`
)



## v0.2.12 =====================================================================
#' @rdname deprecated
#' @export
coerceS4ToList <- function(...) {
    coerceToList(...)
}



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## nocov end