R/Deprecated.R

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

#' Deprecated functions in package \sQuote{derfinder}
#'
#' These functions are provided for compatibility with older version of
#' \sQuote{derfinder} only and will be defunct at the next release.
#'
#' @param fun The name of a function(s) that has advanced arguments in
#' `package`.
#' @param package The name of the package where the function is stored. Only
#' 'derfinder', 'derfinderPlot', and 'regionReport' are accepted.
#' @param browse Whether to open the URLs in a browser.
#'
#' @return A vector of URLs with the GitHub search queries.
#'
#' @details
#'
#' The following functions are deprecated and will be made defunct.
#'
#' \itemize{
#'     \item{advancedArg}{ Not needed now that the advanced arguments are
#'     documented on the help pages of each function.}
#' }
#'
#' @name derfinder-deprecated
#' @export
#'
#' @importFrom utils browseURL
#'
#' @examples
#' ## Open the advanced argument docs for loadCoverage()
#' if (interactive()) {
#'     advancedArg("loadCoverage")
#' } else {
#'     (advancedArg("loadCoverage", browse = FALSE))
#' }
advancedArg <- function(fun, package = "derfinder", browse = interactive()) {
    .Deprecated(msg = "This function is not needed anymore now that the advanced arguments are document in the help pages of each function.")
    stopifnot(package %in% c("derfinder", "derfinderPlot", "regionReport"))

    query_map <- data.frame(
        "fun" = c(
            "analyzeChr", "analyze_chr",
            "annotateRegions", "annotate_regions",
            "calculatePvalues", "calculate_pvalues",
            "calculateStats", "calculate_stats",
            "coerceGR", "coerce_gr",
            "collapseFullCoverage", "collapse_full_coverage",
            "coverageToExon", "coverage_to_exon",
            "createBwSample", "create_bw_sample",
            "filterData", "filter_data",
            "findRegions", "find_regions",
            "fullCoverage", "full_coverage",
            "getRegionCoverage", "get_region_coverage",
            "loadCoverage", "load_coverage",
            "makeGenomicState", "make_genomic_state",
            "mergeResults", "merge_results",
            "preprocessCoverage", "preprocess_coverage",
            "regionMatrix", "region_matrix",
            "sampleDepth", "sample_depth",
            "plotCluster", "plot_cluster",
            "plotOverview", "plot_overview",
            "derfinderReport", "derfinder_report"
        ),
        "query" = rep(c(
            "analyze",
            "annotate",
            "pvalues",
            "stats",
            "coerce",
            "collapse",
            "exon",
            "createBw",
            "filter",
            "find",
            "full,load",
            "get",
            "load",
            "state",
            "merge",
            "preprocess",
            "matrix",
            "depth",
            "cluster",
            "overview",
            "derfinder"
        ), each = 2),
        "repo" = rep(c("derfinder", "derfinderPlot", "regionReport"), c(
            36, 4,
            2
        )),
        stringsAsFactors = FALSE
    )
    repo <- NULL
    query_map <- subset(query_map, repo == package)

    ## Find function
    i <- which(query_map$fun == fun)
    if (length(i) == 0) {
        stop(paste0("Invalid option. 'fun' should match one of '", paste(query_map$fun, collapse = "', '"), "'."))
    }

    ## Build url
    url <- paste0(
        "https://github.com/search?utf8=%E2%9C%93&q=advanced_argument+filename%3A",
        query_map$query[i], "+repo%3Alcolladotor%2F", query_map$repo[i],
        "+path%3A%2FR&type=Code"
    )

    if (browse) {
        for (u in seq_along(url)) {
            browseURL(url[u])
        }
    }
    return(invisible(url))
}