# Automated Classification of Mass Spectra

## Documentation for package ‘MSclassifR’ version 0.5.0

- DESCRIPTION file.

## Help Pages

build_XY_from_peaks | Build design matrix X and response Y from peak intensities
build_X_from_peaks_fast | Build a sample-by-m/z intensity matrix from a list of peaks (fast, C++-backed)
calculate_distance | Function calculating the distance between two vectors.
CitrobacterRKImetadata | Metadata of mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra
CitrobacterRKIspectra | Mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra
d_left_join | Function joining two tables based not on exact matches
fast_cvpvi | Fast cross-validated permutation variable importance (ranger-based)
fast_find_neighbors | Function finding k Nearest Neighbors for each row of a matrix
fast_generate_synthetic | Function generating synthetic examples using SMOTE
fast_mda | Fast MDA-style variable selection using ranger permutation importance
LogReg | Fast supervised classifier with m/z subsetting and optional sampling
LogReg_rf_fast | Fast random-forest classifier with stratified CV and in-fold sampling (ranger, caret-free)
MSclassifR | Automated classification of mass spectra
PeakDetection | Detection of peaks in MassSpectrum objects
PlotSpectra | Plot spectral data with optional peak markers
PredictFastClass | Fast class prediction from peak lists using linear regressions
PredictLogReg | Prediction of the category to which a mass spectrum belongs
SelectionVar | Variable selection using methods based on random forests and others.
SelectionVarStat | Fast feature (m/z) selection using multiple hypothesis testing (LIMMA/ANOVA/Kruskal) with optional class balancing (no/up/down/SMOTE)
SignalProcessing | Signal processing for MALDI-TOF spectra (wrapper to SignalProcessingUltra)
SignalProcessingUltra | Optimized signal processing for MALDI-TOF spectra (parallel + optional C++ alignment)
smote_classif | SMOTE for classification datasets