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Fix some package issues

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This commit is contained in:
Elias Projahn 2021-11-06 13:22:57 +01:00
parent 28f9834984
commit 6d9511fa2e
6 changed files with 41 additions and 19 deletions
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23
R/comparison.R
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@ -24,7 +24,7 @@ compare <- function(ranking, comparison_gene_ids) {
comparison_ranking <- ranking[gene %chin% comparison_gene_ids]
p_value <- wilcox.test(
p_value <- stats::wilcox.test(
x = comparison_ranking[, score],
y = ranking[!gene %chin% comparison_gene_ids, score],
alternative = "greater"
@ -46,10 +46,13 @@ compare <- function(ranking, comparison_gene_ids) {
#' S3 method to print a comparison object.
#'
#' @param x The comparison to print.
#' @param ... Other parameters.
#'
#' @seealso [compare()]
#'
#' @export
print.geposan_comparison <- function(comparison, ...) {
print.geposan_comparison <- function(x, ...) {
cat("geposan comparison:")
cat(sprintf(
paste(
@ -62,14 +65,14 @@ print.geposan_comparison <- function(comparison, ...) {
"\n\n p-value for better ranking: %.4f\n",
sep = ""
),
comparison$mean,
comparison$min,
comparison$max,
comparison$mean_rank,
comparison$first_rank,
comparison$last_rank,
comparison$p_value
x$mean,
x$min,
x$max,
x$mean_rank,
x$first_rank,
x$last_rank,
x$p_value
))
invisible(comparison)
invisible(x)
}