select_cutoff: Select the cutoff for binary cut

In jokergoo/simplifyEnrichment: Simplify Functional Enrichment Results

Select the cutoff for binary cut

Description

Select the cutoff for binary cut

Usage

select_cutoff(mat, cutoff = seq(0.6, 0.98, by = 0.01), verbose = TRUE, ...)

Arguments

mat	A similarity matrix.
cutoff	A list of cutoffs to test. Note the range of the cutoff values should be inside [0.5, 1].
verbose	Whether to print messages.
...	Pass to binary_cut.

Details

Binary cut is applied to each of the cutoff and the clustering results are evaluated by following metrics:

• difference score, calculated by difference_score.

• number of clusters.

• block mean, which is the mean similarity in the blocks in the diagonal of the heatmap.

Examples

mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds",
    package = "simplifyEnrichment"))
select_cutoff(mat)

jokergoo/simplifyEnrichment documentation built on Nov. 3, 2023, 2:57 p.m.