get_sub_clusters {GWENA} | R Documentation

## Detect sub clusters

### Description

Use a partitioning around medoid (PAM, or k-medoid) clustering method to detect clusters into a provided module using the strength matrix of the network

### Usage

    get_sub_clusters(network, seq_k = seq_len(15), fit_plot = TRUE, ...)

### Arguments

`network` | matrix or data.frame, strength of gene co-expression (edge values).
`seq_k` | vector, sequence of k number of cluster to test
`fit_plot` | boolean, does the plot with silhouette coefficient depending on the k tested should be plotted.
`...` | any other parameter compatible with the `pam` function.

### Value

data.frame, a two cols table with the gene id in the first one, and the cluster number assignation in the second one.

### Examples

    df <- kuehne_expr[1:24, 1:350]
    net <- build_net(df, n_threads = 1)
    mods <- detect_modules(df, net$network)
    net_mod_1 <- net$network[mods$modules$`1`, mods$modules$`1`]
    get_sub_clusters(net_mod_1)

[Package GWENA version 1.2.0 Index]