net_cls-mina: Network clustering based on the sparsed adjacacency matrix.

In Guan06/mina: Microbial community dIversity and Network Analysis

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)

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.