Package: MALDIassist 1.0.2

Wonseok Oh

MALDIassist: Mathematical Utilities for MALDI-TOF Mass Spectrometry

Supports matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry workflows from raw Bruker spectra to cohort-level peak matrices. Provides spectrum loading, Savitzky-Golay smoothing, baseline correction (SNIP and TopHat), Gaussian kernel-regression-based peak detection including shoulder peaks, peak-quality assessment, filtering, and cohort feature analysis. Computationally intensive routines are implemented in C++ using 'Rcpp'. The implemented signal-processing methods include those described by Savitzky and Golay (1964) <doi:10.1021/ac60214a047>, Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, Stanford, Bagley and Solomon (2016) <doi:10.1186/s12953-016-0107-8>, and Nadaraya-Watson kernel regression (Nadaraya (1964) <doi:10.1137/1109020>; Watson (1964) <https://www.jstor.org/stable/25049340>).

Authors:Wonseok Oh [aut, cre]

MALDIassist_1.0.2.tar.gz
MALDIassist_1.0.2.zip(r-4.7-x86_64)MALDIassist_1.0.2.zip(r-4.7-arm64)MALDIassist_1.0.2.zip(r-4.6-x86_64)MALDIassist_1.0.2.zip(r-4.6-arm64)MALDIassist_1.0.2.zip(r-4.5-x86_64)
MALDIassist_1.0.2.tgz(r-4.6-x86_64)MALDIassist_1.0.2.tgz(r-4.6-arm64)MALDIassist_1.0.2.tgz(r-4.5-x86_64)MALDIassist_1.0.2.tgz(r-4.5-arm64)
MALDIassist_1.0.2.tar.gz(r-4.7-arm64)MALDIassist_1.0.2.tar.gz(r-4.7-x86_64)MALDIassist_1.0.2.tar.gz(r-4.6-arm64)MALDIassist_1.0.2.tar.gz(r-4.6-x86_64)
MALDIassist_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MALDIassist/json (API)

# Install 'MALDIassist' in R:
install.packages('MALDIassist', repos = c('https://hiows.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hiows/maldiassist/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.30 score 1 stars 223 downloads 27 exports 2 dependencies

Last updated from:e1779d9cf6. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK95
linux-devel-x86_64OK119
source / vignettesOK167
linux-release-arm64OK89
linux-release-x86_64OK113
macos-release-arm64OK177
macos-release-x86_64OK257
macos-oldrel-arm64OK181
macos-oldrel-x86_64OK408
windows-devel-arm64OK389
windows-devel-x86_64OK150
windows-release-arm64OK369
windows-release-x86_64OK103
windows-oldrel-x86_64OK117
wasm-releaseOK106

Exports:align_spectrabuild_kde_spectrabuild_kde_spectrumbuild_matched_matrixcalculate_peak_prominenceestimate_peak_strengthestimate_significancefilter_overlap_mzfilter_peaksfilter_peaks_spectrafind_extremafind_extrema_fastfind_frequent_mzfind_peaksfind_peaks_fastfind_peaks_spectrafind_peaks_spectra_fastget_curvature_funget_gauss_kdeheatmap_matched_matrixload_maldi_spectramatch_peakspreprocess_maldi_spectrasmooth_savitzky_golaysubtract_baselinevisualize_spectravisualize_spectrum

Dependencies:gtoolsRcpp

Readme and manuals

Help Manual

Help pageTopics
MALDIassist: Mathematical utilities for MALDI-TOF mass spectrometryMALDIassist-package MALDIassist
Alignment of MALDI-TOF Spectra to Internal Standardsalign_spectra
Build a Gaussian KDE-Smoothed Spectrumbuild_kde_spectra build_kde_spectrum
Build a Sample-by-Marker Peak Intensity Matrixbuild_matched_matrix
Calculate Peak Prominencecalculate_peak_prominence
Estimate Peak Strengthestimate_peak_strength
Estimate Significant m/z Features Between Two Groupsestimate_significance
Filter Overlapping Frequent m/z Featuresfilter_overlap_mz
Filter Detected Peaks Using Intensity, Prominence, and Peak Strengthfilter_peaks filter_peaks_spectra
Find Local Extrema from First and Second Derivative Functionsfind_extrema
Fast Local Extrema Detection by Sign Changesfind_extrema_fast
Find Frequent m/z Values from a List of Peak Tablesfind_frequent_mz
Detect Ordinary Peaks and Shoulder Peaks Using Weighted Curvaturefind_peaks find_peaks_spectra
Fast Local Peak Detection from a Mass Spectrumfind_peaks_fast find_peaks_spectra_fast
Create a Curvature Function from First and Second Derivative Functionsget_curvature_fun
Create a Gaussian KDE Function for a Mass Spectrumget_gauss_kde
Heatmap of a Sample-by-Marker Matched-Peak Matrixheatmap_matched_matrix
Load Bruker MALDI-TOF MS Spectraload_maldi_spectra
Match Detected Peaks to Reference m/z Valuesmatch_peaks
Preprocess MALDI-TOF Mass Spectrapreprocess_maldi_spectra
Smooth a Spectrum Using the Savitzky-Golay Filtersmooth_savitzky_golay
Subtract Baseline from a Mass Spectrumsubtract_baseline
Visualize One or More Overlaid Mass Spectravisualize_spectra
Visualize a Single Mass Spectrum with Optional Peak Segmentsvisualize_spectrum