Mathematical Utilities for MALDI-TOF Mass Spectrometry

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Documentation for package ‘MALDIassist’ version 1.0.2

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MALDIassist-package MALDIassist: Mathematical utilities for MALDI-TOF mass spectrometry
align_spectra Alignment of MALDI-TOF Spectra to Internal Standards
build_kde_spectra Build a Gaussian KDE-Smoothed Spectrum
build_kde_spectrum Build a Gaussian KDE-Smoothed Spectrum
build_matched_matrix Build a Sample-by-Marker Peak Intensity Matrix
calculate_peak_prominence Calculate Peak Prominence
estimate_peak_strength Estimate Peak Strength
estimate_significance Estimate Significant m/z Features Between Two Groups
filter_overlap_mz Filter Overlapping Frequent m/z Features
filter_peaks Filter Detected Peaks Using Intensity, Prominence, and Peak Strength
filter_peaks_spectra Filter Detected Peaks Using Intensity, Prominence, and Peak Strength
find_extrema Find Local Extrema from First and Second Derivative Functions
find_extrema_fast Fast Local Extrema Detection by Sign Changes
find_frequent_mz Find Frequent m/z Values from a List of Peak Tables
find_peaks Detect Ordinary Peaks and Shoulder Peaks Using Weighted Curvature
find_peaks_fast Fast Local Peak Detection from a Mass Spectrum
find_peaks_spectra Detect Ordinary Peaks and Shoulder Peaks Using Weighted Curvature
find_peaks_spectra_fast Fast Local Peak Detection from a Mass Spectrum
get_curvature_fun Create a Curvature Function from First and Second Derivative Functions
get_gauss_kde Create a Gaussian KDE Function for a Mass Spectrum
heatmap_matched_matrix Heatmap of a Sample-by-Marker Matched-Peak Matrix
load_maldi_spectra Load Bruker MALDI-TOF MS Spectra
MALDIassist MALDIassist: Mathematical utilities for MALDI-TOF mass spectrometry
match_peaks Match Detected Peaks to Reference m/z Values
preprocess_maldi_spectra Preprocess MALDI-TOF Mass Spectra
smooth_savitzky_golay Smooth a Spectrum Using the Savitzky-Golay Filter
subtract_baseline Subtract Baseline from a Mass Spectrum
visualize_spectra Visualize One or More Overlaid Mass Spectra
visualize_spectrum Visualize a Single Mass Spectrum with Optional Peak Segments