adj,mina,ANY-method {mina}R Documentation

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

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)

[Package mina version 1.0.0 Index]