adj-matrix: 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 matrix as input.

Usage

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

## S4 method for signature 'matrix,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	(optional) The asymtotic P-values, only applicable for Pearson and Spearman methods with 'mina' object as input, alwasy FALSE here.
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

y The adjacency matrix.

Examples

asv_norm <- norm_tab(maize_asv2, method = "raref", depth = 1000)
asv_adj <- adj(asv_norm, method = "pearson")

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