R/resultsTables-methods.R

In acidgenomics/r-deseqanalysis: Acid Genomics DESeq2 Analysis Utilities

#' @name resultsTables
#' @inherit AcidGenerics::resultsTables
#' @note Updated 2022-05-24.
#'
#' @inheritParams params
#' @inheritParams results
#' @inheritParams AcidRoxygen::params
#' @param ... Additional arguments.
#'
#' @details
#' Generate tables summarizing the differential expression, with subsets for
#' differentially expressed genes (DEGs). DEG tables (i.e. everything except the
#' `all` table), are arranged by adjusted *P* value.
#'
#' @note It is generally recommended to not apply post hoc log fold change
#' cutoffs. If a specific effect size is desired, instead run
#' `DESeq2::results()` using the `lfcThreshold` parameter. Refer to the DESeq2
#' documentation and vignette for details.
#'
#' @section Tables:
#'
#' - `all`: All genes, including genes without an adjusted *P* value. This table
#' is unmodified, and the rows have not been re-arranged or subset. It is
#' suitable for gene set enrichment analysis (GSEA).
#' - `up`: Upregulated genes.
#' - `down`: Downregulated genes.
#' - `both`: Bidirectional DEGs (up- and down-regulated). This table can be
#' used for overrepresentation testing but should NOT be used for GSEA.
#'
#' @return `DFrameList`.
#' Named list containing subsets of `DESeqResults`.
#'
#' @examples
#' data(deseq)
#'
#' ## DESeqAnalysis ====
#' x <- resultsTables(deseq, i = 1L)
#' print(x)
NULL



## Updated 2023-12-18.
`resultsTables,DESeqAnalysis` <- # nolint
    function(object,
             i,
             alphaThreshold = NULL,
             baseMeanThreshold = NULL,
             lfcThreshold = NULL,
             extra = TRUE) {
        assert(validObject(object))
        resultsTables(
            object = results(object = object, i = i, extra = extra),
            alphaThreshold = ifelse(
                test = is.null(alphaThreshold),
                yes = alphaThreshold(object),
                no = alphaThreshold
            ),
            baseMeanThreshold = ifelse(
                test = is.null(baseMeanThreshold),
                yes = baseMeanThreshold(object),
                no = baseMeanThreshold
            ),
            lfcThreshold = ifelse(
                test = is.null(lfcThreshold),
                yes = lfcThreshold(object),
                no = lfcThreshold
            )
        )
    }



## Updated 2022-05-24.
`resultsTables,DESeqResults` <- # nolint
    function(object,
             alphaThreshold = NULL,
             baseMeanThreshold = NULL,
             lfcThreshold = NULL) {
        both <- deg(
            object = object,
            direction = "both",
            alphaThreshold = alphaThreshold,
            baseMeanThreshold = baseMeanThreshold,
            lfcThreshold = lfcThreshold
        )
        if (!hasLength(both)) {
            out <- list("all" = object)
        } else {
            up <- deg(
                object = object,
                direction = "up",
                alphaThreshold = alphaThreshold,
                baseMeanThreshold = baseMeanThreshold,
                lfcThreshold = lfcThreshold
            )
            down <- deg(
                object = object,
                direction = "down",
                alphaThreshold = alphaThreshold,
                baseMeanThreshold = baseMeanThreshold,
                lfcThreshold = lfcThreshold
            )
            out <- list(
                "all" = object,
                "up" = object[up, , drop = FALSE],
                "down" = object[down, , drop = FALSE],
                "both" = object[both, , drop = FALSE]
            )
            out <- Filter(f = hasRows, x = out)
        }
        out <- DataFrameList(out)
        out
    }



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

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