Proteomics Quality Control

Sample Quality Metrics

import pandas as pd
import numpy as np

def sample_qc_metrics(intensity_matrix):
    '''Calculate per-sample QC metrics'''
    metrics = pd.DataFrame(index=intensity_matrix.columns)
    metrics['n_proteins'] = intensity_matrix.notna().sum()
    metrics['median_intensity'] = intensity_matrix.median()
    metrics['mean_intensity'] = intensity_matrix.mean()
    metrics['cv'] = intensity_matrix.std() / intensity_matrix.mean()
    metrics['missing_pct'] = 100 * intensity_matrix.isna().sum() / len(intensity_matrix)
    return metrics