select_cutoff: Select the cutoff for binary cut

In jokergoo/simplifyGO: 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 = se_opt$verbose,
  ...
)

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 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/simplifyGO documentation built on Sept. 18, 2024, 9:45 p.m.