net_cls,mina,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 'mina,ANY'
    net_cls(x, method, cutoff = 0.4, neg = FALSE, ...)

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

### Arguments

`x` | An object of class 'mina' with 'adj' defined.
`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

x The same 'mina' class with @cls added.

### Examples

    maize <- new("mina", tab = maize_asv2, des = maize_des2)
    maize <- norm_tab(maize, method = "raref", depth = 1000)
    maize <- fit_tabs(maize)
    maize <- adj(maize, method = "spearman")
    maize <- net_cls(maize, method = "mcl", cutoff = 0.4, neg = FALSE)
    maize <- net_cls(maize, method = "ap", cutoff = 0.4, neg = FALSE)

[Package mina version 1.2.0 Index]