R/importPairwiseContrasts.R

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

#' Import pairwise contrasts from a file
#'
#' @export
#' @note Updated 2022-05-17.
#'
#' @inheritParams AcidRoxygen::params
#'
#' @param groupCol `character(1)`.
#' Group column name in `colData()` of
#' `DESeqDataSet`. Corresponds to value in `design()`.
#'
#' @param numeratorCol `character(1)`.
#' Numerator column name in contrasts file.
#'
#' @param denominatorCol `character(1)`.
#' Denominator column name in contrasts file.
#'
#' @param namesCol `character(1)`.
#' Column in contrasts file to used to define the names of the contrast list.
#' Values will be sanitized using `snakeCase()`.
#'
#' @seealso `DESeq2::results()`.
#'
#' @return `list`.
#' Named list of pairwise character vectors containing: "group", "numerator",
#' "denominator".
#'
#' @examples
#' file <- system.file("extdata", "contrasts.csv", package = "DESeqAnalysis")
#' x <- importPairwiseContrasts(file)
#' print(x)
importPairwiseContrasts <-
    function(file,
             groupCol = "group",
             numeratorCol = "numerator",
             denominatorCol = "denominator",
             namesCol = "description") {
        assert(
            isAFile(file),
            isString(groupCol),
            isString(numeratorCol),
            isString(denominatorCol)
        )
        data <- import(file)
        assert(
            isSubset(
                x = c(numeratorCol, denominatorCol, namesCol),
                y = colnames(data)
            )
        )
        list <- Map(
            numerator = data[["numerator"]],
            denominator = data[["denominator"]],
            MoreArgs = list("group" = groupCol),
            f = function(group, numerator, denominator) {
                c(
                    "group" = group,
                    "numerator" = numerator,
                    "denominator" = denominator
                )
            }
        )
        names(list) <- snakeCase(data[[namesCol]])
        list
    }