Package: MassSpecWavelet 1.73.0

Sergio Oller Moreno

MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.

Authors:Pan Du [aut], Warren Kibbe [aut], Simon Lin [aut], Sergio Oller Moreno [aut, cre]

# Install 'MassSpecWavelet' in R:

install.packages('MassSpecWavelet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zeehio/massspecwavelet/issues

Datasets:

exampleMS - An example mass spectrum

On BioConductor:MassSpecWavelet-1.71.0(bioc 3.20)MassSpecWavelet-1.70.0(bioc 3.19)

immunooncology massspectrometry proteomics peakdetection

9.07 score 8 stars 15 packages 35 scripts 3.3k downloads 19 mentions 13 exports 0 dependencies

Last updated 23 days agofrom:4f19a4c7c3. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	NOTE	Oct 30 2024
R-4.5-linux-x86_64	NOTE	Oct 30 2024
R-4.4-win-x86_64	NOTE	Oct 30 2024
R-4.4-mac-x86_64	NOTE	Oct 30 2024
R-4.4-mac-aarch64	NOTE	Oct 30 2024
R-4.3-win-x86_64	NOTE	Oct 30 2024
R-4.3-mac-x86_64	NOTE	Oct 30 2024
R-4.3-mac-aarch64	NOTE	Oct 30 2024

Exports:cwt getLocalMaximumCWT getRidge getRidgeLength identifyMajorPeaks localMaximum mexh peakDetectionCWT plotLocalMax plotPeak plotRidgeList prepareWavelets tuneInPeakInfo

Dependencies:

Finding local maxima with MassSpecWavelet

Sergio Oller

Rendered fromFindingLocalMaxima.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-10-10
Started: 2022-10-06

Using the MassSpecWavelet package

Pan Du, Warren A. Kibbe, Simon Lin

Rendered fromMassSpecWavelet.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-01-30
Started: 2022-04-04

Help page	Topics
Peak detection of mass spectrum by Wavelet transform based methods	MassSpecWavelet-package MassSpecWavelet
Continuous Wavelet Transform (CWT)	cwt
An example mass spectrum	exampleMS
Find local maxima and return the size of the window where they are maximum.	findLocalMaxWinSize
Identify the local maximum of each column in 2-D CWT coefficients matrix	getLocalMaximumCWT
Identify ridges based on the local maximum matrix	getRidge
Estimate the length of the ridge	getRidgeLength
Get the CWT coefficient values corresponding to the peak ridge	getRidgeValue
Identify peaks based on the ridges in 2-D CWT coefficient matrix	identifyMajorPeaks
Identify local maximum within a slide window.	localMaximum
The mexican hat function	mexh
Match m/z index to m/z value with a certain error range	mzInd2vRange
Match m/z value to m/z index with a certain error range	mzV2indRange
The main function of peak detection by CWT based pattern matching	peakDetectionCWT
Plot the local maximum matrix	plotLocalMax
Plot the identified peaks over the spectrum	plotPeak
Plot the ridge list	plotRidgeList
Prepare daughter wavelets for faster CWT	prepareWavelets
smooth (denoise) the spectrum by DWT (Discrete Wavelet Transform)	smoothDWT
Tune in the peak information: peak position and peak scale	tuneInPeakInfo

Package: MassSpecWavelet 1.73.0

MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Finding local maxima with MassSpecWavelet

Using the MassSpecWavelet package

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)