select_cutoff {simplifyEnrichment}R Documentation

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:

Examples


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


[Package simplifyEnrichment version 1.3.0 Index]