Summarize significant proteins per comparison and species

Generates a summary table with counts of significant and non-significant proteins broken down by species and direction (up/down), plus derived percentages and ratios.

Usage

.summarize_significant_proteins(classified_df)

Arguments

classified_df

Data frame from .classify_all_comparisons() with columns: Comparison, Species, logFC, truth, predicted, classification, is_significant and direction_error

Value

Data frame with per-comparison summary

Details

Significance is read from the is_significant column rather than recomputed, so this table can never disagree with the classification it summarizes. It used to apply only p <= alpha, ignoring lfc_thr entirely, which made the counts here larger than the ones behind the metrics whenever a fold-change threshold was in force.