Context and FDR Estimation Documentation

This module implements context-specific inference workflows for genes, proteins, peptides, and glycopeptides in targeted proteomics and glycoproteomics data analysis.

It provides functions for statistical error estimation, FDR control, and reporting at different levels of biological organization. The workflows support global, experiment-wide, and run-specific contexts.

Functions:

  • statistics_report: Generates error statistics and updates the input data with FDR-related metrics.

  • infer_genes: Performs gene-level inference based on the specified context.

  • infer_proteins: Performs protein-level inference based on the specified context.

  • infer_peptides: Performs peptide-level inference based on the specified context.

  • infer_glycopeptides: Performs glycopeptide-level inference based on the specified context.

statistics_report

Generates error statistics and updates the input data with FDR-related metrics.

infer_peptides

Performs peptide-level inference based on the specified context.

infer_glycopeptides

Performs glycopeptide-level inference based on the specified context.

infer_proteins

Performs protein-level inference based on the specified context.

infer_genes

Performs gene-level inference based on the specified context.