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 1.1.11 Index]