Generates lists of DAMs (Differentially Accumulated Metabolites) for each comparison in the mmo object

This function generates lists of upregulated and downregulated DAMs for each pairwise comparison in the mmo object. It uses log2 fold change and adjusted p-value thresholds to determine significance. Make sure to run PairwiseComp() for all desired comparisons before using this function.

Usage

GetDAMs(mmo, fc_cutoff = 0.5849625, pval_cutoff = 0.05, use_padj = TRUE)

Arguments

mmo

The mmo object with pairwise comparison matrix

fc_cutoff

The threshold of log2 fold change to be considered significant (default: 0.5849625, which is log2(1.5))

pval_cutoff

The threshold of adjusted p-value to be considered significant (default: 0.05)

use_padj

Boolean value indicating whether to use adjusted p-value (default: TRUE)

Value

A list containing two lists: DAMs_up and DAMs_down

Examples

if (FALSE) {
dams <- GetDAMs(mmo, fc_cutoff = 0.5849625, pval_cutoff = 0.05)
dams_up <- dams$DAMs_up
dams_down <- dams$DAMs_down
}