Remove redundant pathways

Greedy redundancy filter: pathways are visited from most to least significant and a pathway is dropped when its gene-set Jaccard similarity with an already retained pathway is at least jaccard_threshold.

Usage

mx_pathway_dedup(pathway_results, gene_sets = NULL, jaccard_threshold = 0.5)

Arguments

pathway_results

A data.frame with pathway_id and a p-value column (padj or meta_padj).

gene_sets

The named list of gene sets used for the enrichment. When NULL, results are returned unchanged with a warning.

jaccard_threshold

Numeric. Default: 0.5.

Value

The filtered data.frame, ordered by significance.

Examples

sets <- list(A = letters[1:10], B = letters[1:9], C = letters[15:25])
res  <- data.frame(pathway_id = c("A", "B", "C"), padj = c(0.01, 0.02, 0.03))
mx_pathway_dedup(res, gene_sets = sets)
#>   pathway_id padj
#> 1          A 0.01
#> 3          C 0.03