R/correlation-methods.R

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

#' Correlation
#'
#' @name correlation
#' @inherit AcidExperiment::correlation
#' @note Updated 2021-03-15.
#'
#' @inheritParams AcidRoxygen::params
#' @param ... Additional arguments.
#'
#' @param col `character(1)`.
#' Column name.
#'
#' @examples
#' data(deseq)
#'
#' ## DESeqAnalysis ====
#' correlation(deseq, i = 1L, j = 2L)
NULL



.method <- formals(S4Vectors::cor)[["method"]]



## Updated 2019-11-08.
`correlation,DESeqResults,DESeqResults` <- # nolint
    function(x, y, col = "log2FoldChange", method) {
        assert(
            hasRownames(x),
            hasRownames(y),
            areIntersectingSets(x = rownames(x), y = rownames(y)),
            isString(col),
            isSubset(col, colnames(x)),
            isSubset(col, colnames(y))
        )
        method <- match.arg(method)
        ## Ensure that we're only comparing genes in common.
        keep <- intersect(x = rownames(x), y = rownames(y))
        data <- DataFrame(
            x = x[keep, col, drop = TRUE],
            y = y[keep, col, drop = TRUE],
            row.names = rownames(x)
        )
        ## Ensure that no NA values propagate.
        data <- data[complete.cases(data), , drop = FALSE]
        correlation(x = data[["x"]], y = data[["y"]], method = method)
    }

formals(`correlation,DESeqResults,DESeqResults`)[["method"]] <- # nolint
    .method



## Updated 2020-08-05.
`correlation,DESeqAnalysis,missing` <- # nolint
    function(x,
             y = NULL,
             i,
             j,
             col = "log2FoldChange",
             method) {
        assert(!identical(i, j))
        method <- match.arg(method)
        correlation(
            x = results(object = x, i = i),
            y = results(object = x, i = j),
            method = method
        )
    }

formals(`correlation,DESeqAnalysis,missing`)[["method"]] <- # nolint
    .method



rm(.method)



#' @rdname correlation
#' @export
setMethod(
    f = "correlation",
    signature = signature(
        x = "DESeqResults",
        y = "DESeqResults"
    ),
    definition = `correlation,DESeqResults,DESeqResults`
)

#' @rdname correlation
#' @export
setMethod(
    f = "correlation",
    signature = signature(
        x = "DESeqAnalysis",
        y = "missingOrNULL"
    ),
    definition = `correlation,DESeqAnalysis,missing`
)