API Reference

run_efdr_analysis(parquet_files::Vector{String}, library_path::String; kwargs...)

Run empirical FDR analysis at the precursor level.

The function modifies the results DataFrame by adding pairing information columns:

• is_original: Boolean indicating if peptide is original (true) or entrapment (false)
• pair_id: Integer ID linking original/entrapment pairs
• entrap_label: Integer label (0=original, 1=entrapment) for EFDR
• complement_score: Plex-specific score of the paired peptide
• complement_indices: Deprecated column for backward compatibility

Arguments

• parquet_files: Vector of paths to Parquet files with PSM results
• library_path: Path to TSV file with spectral library

Keyword Arguments

• output_dir: Output directory (default: "efdr_output")
• score_col: Score column name (default: :PredVal)
• global_qval_threshold: Global q-value filter threshold (default: 1.0 = no filter)
• local_qval_threshold: Local q-value filter threshold (default: 0.05)
• r_lib: Library to real entrapment ratio (default: 1.0)
• show_progress: Show progress bars (default: true)

Returns

• DataFrame with EFDR columns added

run_protein_efdr_analysis(parquet_files::Vector{String}, library_path::String; kwargs...)

Run empirical FDR analysis at the protein level following the notebook implementation.

The function modifies the protein DataFrame by adding pairing information columns:

• is_original: Boolean indicating if protein is original (true) or entrapment (false)
• pair_id: Integer ID linking original/entrapment pairs
• entrap_label: Integer label (0=original, 1=entrapment) for EFDR
• complement_score: Plex-specific score of the paired protein
• complement_indices: Deprecated column for backward compatibility

Arguments

• parquet_files: Vector of paths to Parquet files with PSM results
• library_path: Path to TSV file with spectral library

Keyword Arguments

• output_dir: Output directory (default: "efdr_output")
• score_col: Score column name (default: :PredVal)
• global_qval_threshold: Global q-value filter threshold (default: 1.0 = no filter)
• local_qval_threshold: Local q-value filter threshold (default: 0.05)
• r_lib: Library to real entrapment ratio (default: 1.0)
• show_progress: Show progress bars (default: true)

Returns

• DataFrame with protein-level EFDR analysis

load_parquet(filepath::String)

Load a single Parquet file containing PSM results.

Arguments

• filepath: Path to the Parquet file

Returns

• DataFrame with PSM results

calculate_qvalues!(df::AbstractDataFrame; score_col=:PredVal, decoy_col=:decoy, sort_df=true)

Calculate local q-values and add to DataFrame.

Arguments

• df: DataFrame to process
• score_col: Score column name
• decoy_col: Decoy column name
• sort_df: Whether to sort the DataFrame (default: true)

calculate_qvalues_per_file!(df::AbstractDataFrame; score_col=:PredVal, file_col=:file_name)

Calculate q-values separately for each file in the dataframe. Adds :localqvalue and :globalqvalue columns.

Arguments

• df: DataFrame with PSM results
• score_col: Score column name (default: :PredVal)
• file_col: File identifier column (default: :file_name)

calculate_global_qvalues!(df::AbstractDataFrame; score_col=:PredVal)

Calculate global q-values (best per precursor). Adds :global_qvalue column to the dataframe.

monotonize!(values::AbstractVector{T}) where T<:AbstractFloat

Ensure FDR values are monotonically non-decreasing. Works in-place by traversing backwards through sorted results.

Algorithm

Starting from the end (worst scores), ensures each FDR is at least as large as the FDR of better-scoring results.

monotonize!(values::AbstractVector{Union{Missing, T}}) where T<:AbstractFloat

Handle missing values in monotonization.

compute_pairing_vectors!(library_df::DataFrame, results_df::DataFrame; kwargs...)

Add plex-aware pairing information directly to the results DataFrame.

Modifies results_df by adding the following columns:

• :is_original - Bool: true if peptide is original, false if entrapment
• :pair_id - Int: ID linking original/entrapment pairs from library
• :entrap_label - Int: 0 for original, 1 for entrapment (used in EFDR)
• :complement_score - Float32: plex & file-specific score of paired peptide (-1 if no pair)
• :complement_indices - Int: deprecated, always -1 (kept for compatibility)

The complement scores respect both file and plex boundaries, meaning the same peptide in different plexes can have different complement scores.

Arguments

• library_df: Library DataFrame with entrapment pairs
• results_df: Results DataFrame to modify (must have file_name and channel columns)

Keyword Arguments

• lib_seq_col: Library sequence column (default: :PeptideSequence)
• lib_charge_col: Library charge column (default: :PrecursorCharge)
• lib_entrap_col: Library entrapment group column (default: :EntrapmentGroupId)
• lib_pair_col: Library pair ID column (default: :PrecursorIdx)
• results_seq_col: Results sequence column (default: :stripped_seq)
• results_charge_col: Results charge column (default: :z)
• channel_col: Channel/plex column (default: :channel)
• score_col: Score column (default: :PredVal)
• file_col: File name column (default: :file_name)
• show_progress: Show progress bars (default: true)

Returns

• Modified results_df with new columns added

plot_combined_efdr(df::DataFrame; kwargs...)

Create a plot showing only the combined EFDR results.

Arguments

• df: DataFrame with EFDR results
• output_path: Output file path (default: "combined_efdr.pdf")
• fdr_col: FDR column name (default: :local_qvalue)
• efdr_col: EFDR column name (default: :combinedentrapmentfdr)

plot_paired_efdr(df::DataFrame; kwargs...)

Create a plot showing only the paired EFDR results.

Arguments

• df: DataFrame with EFDR results
• output_path: Output file path (default: "paired_efdr.pdf")
• fdr_col: FDR column name (default: :local_qvalue)
• efdr_col: EFDR column name (default: :pairedentrapmentfdr)

plot_efdr_comparison_both_methods(df::DataFrame; kwargs...)

Create a comparison plot showing both combined and paired EFDR methods.

Arguments

• df: DataFrame with both combined and paired EFDR results
• output_path: Output file path (default: "efdrcomparisonboth_methods.pdf")
• fdr_col: FDR column name (default: :local_qvalue)
• combined_efdr_col: Combined EFDR column name (default: :combinedentrapmentfdr)
• paired_efdr_col: Paired EFDR column name (default: :pairedentrapmentfdr)

generate_analysis_report(df::DataFrame, output_dir::String; kwargs...)

Generate a markdown report with embedded plots and analysis summary.

Arguments

• df: DataFrame with EFDR results
• output_dir: Directory to save report and plots
• paired_df: Optional DataFrame with paired EFDR results (if calculated separately)