This function performs differential expression analysis using limma-based methods (limma_protein_DE or limma_protein_DE_pair), and returns a data.frame containing: - rowData(se) - expression matrix - DEG statistics - group median expression values
Usage
se2DEGs(
se,
compare_col = "condition",
ref = NULL,
cmp = NULL,
pair_col = NULL,
logFC_cutoff = 1,
adj_p_cutoff = 0.05
)Arguments
- se
A SummarizedExperiment object.
- compare_col
Column in colData(se) used to define groups.
- ref
Reference group (optional).
- cmp
Comparison group (optional).
- pair_col
Optional column for paired analysis.
- logFC_cutoff
Absolute logFC threshold for DEG classification.
- adj_p_cutoff
Adjusted p-value threshold for DEG classification.