mirror of
https://github.com/johrpan/geposan.git
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89 lines
2.5 KiB
R
89 lines
2.5 KiB
R
#' Compare a set of genes with the ranking.
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#'
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#' @param ranking A ranking created using [ranking()].
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#' @param comparison_gene_ids IDs of the genes of interest.
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#'
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#' @returns A comparison object with the following items:
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#' \describe{
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#' \item{`quantiles`}{A `data.table` containing quantile values for the
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#' score, rank and percentile of the comparison genes.
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#' }
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#' \item{`mean_score`}{The mean score of the genes.}
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#' \item{`mean_rank`}{The mean rank of the genes.}
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#' \item{`mean_percentile`}{The mean percentile of the genes.}
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#' \item{`test_result`}{Results of applying a Wilcoxon rank sum test.}
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#' }
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#'
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#' @export
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compare <- function(ranking, comparison_gene_ids) {
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if (!inherits(ranking, "geposan_ranking")) {
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stop("Invalid ranking. Use geposan::ranking().")
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}
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comparison_ranking <- ranking[gene %chin% comparison_gene_ids]
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quantiles <- data.table(
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quantile = c("0%", "25%", "50%", "75%", "100%"),
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score = stats::quantile(comparison_ranking[, score]),
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rank = stats::quantile(
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comparison_ranking[, rank],
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probs = seq(1, 0, -0.25)
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),
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percentile = stats::quantile(comparison_ranking[, percentile])
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)
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test <- stats::wilcox.test(
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x = comparison_ranking[, score],
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y = ranking[!gene %chin% comparison_gene_ids, score],
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conf.int = TRUE
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)
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structure(
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list(
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quantiles = quantiles,
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mean_score = comparison_ranking[, mean(score)],
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mean_rank = comparison_ranking[, mean(rank)],
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mean_percentile = comparison_ranking[, mean(percentile)],
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test_result = test
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),
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class = "geposan_comparison"
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)
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}
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#' S3 method to print a comparison object.
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#'
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#' @param x The comparison to print.
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#' @param ... Other parameters.
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#'
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#' @seealso [compare()]
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#'
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#' @export
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print.geposan_comparison <- function(x, ...) {
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cat("geposan comparison:\n\n")
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quantiles_formatted <- x$quantiles[, .(
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"Quantile" = quantile,
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"Score" = round(score, 3),
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"Rank" = rank,
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"Percentile" = paste0(
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format(round(percentile * 100, 1), nsmall = 1),
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"%"
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)
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)]
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print(quantiles_formatted, row.names = FALSE)
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cat(glue::glue(
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"\n",
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"\n Mean score: {num(x$mean_score, 3)}",
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"\n Mean rank: {num(x$mean_rank, 1)}",
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"\n Mean percentile: {num(x$mean_percentile * 100, 2)}",
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"\n",
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"\n Estimated difference in medians: ",
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"{num(x$test$conf.int[1], 2)} to {num(x$test$conf.int[2], 2)}",
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"\n Confidence level: 95%",
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"\n p-value: {num(x$test$p.value, 4)}"
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))
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invisible(x)
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}
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