adj-mina: Calculate the adjacency matrix of 'norm' by correlation with...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Calculate the adjacency matrix of 'norm' by correlation with 'mina' class object as input.

Usage

## S4 method for signature 'mina,ANY'
adj(x, method, sig = FALSE, threads = 80, nblocks = 400, ...)

## S4 method for signature 'mina,character'
adj(x, method, sig = FALSE, threads = 80, nblocks = 400, ...)

Arguments

x	An object of the class mina with 'norm' defined or a 'norm' matrix.
method	The correlation coeffient used for adjacacency matrix.
sig	The asymtotic P-values, only applicable for Pearson and Spearman methods, FALSE by default.
threads	The number of threads used for parallel running, 80 by default.
nblocks	The number of row/column for splitting sub-matrix, 400 by default.
...	Additional parameters.

Value

x The same 'mina' object with 'adj' added.

Examples

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref")
maize <- fit_tabs(maize)
maize <- adj(maize, method = "spearman", sig = FALSE)

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