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:

- 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)

[Package simplifyEnrichment version 1.4.0 Index]