net_cls,matrix,ANY-method {mina} | R Documentation

## Network clustering based on the sparsed adjacacency matrix.

### Description

Network clustering based on the sparsed adjacacency matrix.

### Usage

    ## S4 method for signature 'matrix,ANY'
    net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)

    ## S4 method for signature 'matrix,character'
    net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)

### Arguments

`x` | Adjacency matrix used for clustering.
`method` | The clustering method used.
`cutoff` | The cutoff for the sparsed adjacacency matrix, default 0.4.
`neg` | Whether to keep the negative edges, cannot be TRUE when using 'mcl' for clustering. Default FALSE.
`...` | Additional parameters.

### Value

y The cluster table.

### Examples

    asv_norm <- norm_tab(maize_asv2, method = "raref", depth = 1000)
    asv_adj <- adj(asv_norm, method = "spearman")
    asv_cls <- net_cls(asv_adj, method = "mcl")

[Package mina version 1.2.0 Index]