get_sub_clusters {GWENA} | R Documentation |
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
get_sub_clusters(network, seq_k = seq_len(15), fit_plot = TRUE, ...)
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
|
data.frame, a two cols table with the gene id in the first one, and the cluster number assignation in the second one.
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)