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September 9, 2024 12:39
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MALDI TOF MS baseline correction and normalisation functions for antibiotic resistance prediction
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| # Function for baseline correction using a simple rolling minimum | |
| import numpy as np | |
| from scipy.signal import savgol_filter | |
| def baseline_correction(intensities, window_size=50, poly_order=3): | |
| baseline = savgol_filter(intensities, window_length=window_size, polyorder=poly_order) | |
| corrected_intensities = intensities - baseline | |
| corrected_intensities[corrected_intensities < 0] = 0 # Ensuring no negative intensities | |
| return corrected_intensities | |
| # Function for total ion current (TIC) normalization | |
| def tic_normalization(intensities): | |
| total_ion_current = np.sum(intensities) | |
| normalized_intensities = intensities / total_ion_current | |
| return normalized_intensities | |
| # Perform baseline correction | |
| corrected_intensities = baseline_correction(intensities) | |
| # Perform TIC normalization on baseline-corrected data | |
| normalized_intensities = tic_normalization(corrected_intensities) |
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