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)
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)
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
}