This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/MsCoreUtils

Package: MsCoreUtils 1.25.4

RforMassSpectrometry Package Maintainer

MsCoreUtils: Core Utils for Mass Spectrometry Data

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Authors:RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut], Johannes Rainer [aut], Sebastian Gibb [aut], Philippine Louail [aut], Adriano Rutz [aut], Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb], Josep Maria Badia Aparicio [ctb], Michael Witting [ctb], Samuel Wieczorek [ctb], Roger Gine Bertomeu [ctb], Mar Garcia-Aloy [ctb], Gabriele Tomè [ctb], Muyao Xi [ctb]

# Install 'MsCoreUtils' in R:

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

Bug tracker:https://github.com/rformassspectrometry/mscoreutils/issues

On BioConductor:MsCoreUtils-1.25.4(bioc 3.24)MsCoreUtils-1.24.0(bioc 3.23)

infrastructure proteomics massspectrometry metabolomics bioconductor mass-spectrometry utils

10.36 score 17 stars 83 packages 83 scripts 80 exports 7 dependencies

Last updated from:5fef351964. Checks:13 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	200
linux-devel-x86_64	OK	213
source / vignettes	OK	193
linux-release-arm64	OK	212
linux-release-x86_64	OK	214
macos-release-arm64	OK	197
macos-release-x86_64	OK	233
macos-oldrel-arm64	OK	171
macos-oldrel-x86_64	OK	339
windows-devel	OK	191
windows-release	OK	165
windows-oldrel	OK	156
wasm-release	OK	149

Exports:%between%aggregate_by_matrix aggregate_by_vector asInteger between bin breaks_ppm closest coefMA coefSG coefWMA colCounts colMeansMat colSumsMat common common_path entropy estimateBaseline estimateBaselineConvexHull estimateBaselineMedian estimateBaselineSnip estimateBaselineTopHat force_sorted formatRt getImputeMargin gnps gnps_chain_dp gnps_r group group_mz_int i2index impute_bpca impute_fun impute_knn impute_matrix impute_min impute_MinDet impute_MinProb impute_mixed impute_mle impute_neighbour_average impute_QRILC impute_RF impute_with impute_zero imputeMethods isPeaksMatrix join join_gnps join_gnps_r localMaxima maxi medianPolish navdist ndotproduct nentropy neuclidean noise normalize_matrix normalizeMethods nspectraangle ppm rbindFill reduce refineCentroids retry rla robustSummary rowRla rt2character rt2numeric smooth sumi validPeaksMatrix valleys vapply1c vapply1d vapply1l which.first which.last

Dependencies:BiocGenerics clue cluster generics MASS Rcpp S4Vectors

Core Utils for Mass Spectrometry Data

Introduction | Examples | Contributions | Session information | References

Rendered fromMsCoreUtils.Rmdusingknitr::rmarkdown

Last update: 2026-03-13
Started: 2020-04-05

Help page	Topics
Aggreagate quantitative features	aggregate aggregate_by_matrix aggregate_by_vector colMeansMat colSumsMat
Range helper functions	%between% between
Binning	bin
Sequence with increasing difference between elements	breaks_ppm
Relaxed Value Matching	closest common join
Coerce functions	asInteger coerce
Counts the number of features	colCounts
Extract the common file path	common_path
Spectra Distance/Similarity Measurements	distance dotproduct navdist ndotproduct neuclidean nspectraangle
Spectral entropy	entropy nentropy
Estimates the Baseline of a Mass Spectrum	estimateBaseline estimateBaselineConvexHull estimateBaselineMedian estimateBaselineSnip estimateBaselineTopHat
Forcing a numeric vector into a monotonously increasing sequence.	force_sorted
Optimized GNPS Modified Cosine Similarity via Chain-DP	gnps_chain_dp
GNPS spectrum similarity scores	gnps gnps_r join_gnps join_gnps_r
Grouping of numeric values by similarity	group
Grouping of numeric values by similarity of m/z and intensity	group_mz_int
Input parameter check for subsetting operations	i2index
Quantitative mass spectrometry data imputation	getImputeMargin imputeMethods impute_bpca impute_fun impute_knn impute_matrix impute_min impute_MinDet impute_MinProb impute_mixed impute_mle impute_neighbour_average impute_QRILC impute_RF impute_with impute_zero
Check functions	isPeaksMatrix
Local Maxima	localMaxima
Maximum MS Intensity Value	maxi
Return the Median Polish (Robust Twoway Decomposition) of a matrix	medianPolish
Noise Estimation	noise
Quantitative data normalisation	normalizeMethods normalize_matrix
PPM - Parts per Million	ppm
Combine R Objects by Row	rbindFill
Reduce overlapping numeric ranges to disjoined ranges	reduce
Refine Peak Centroids	refineCentroids
Retry expression on failure	retry
Calculate relative log abundances	rla rowRla
Return the Robust Expression Summary of a matrix	robustSummary
Format Retention Time	formatRt rt2character rt2numeric
Smoothing	coefMA coefSG coefWMA smooth
Summing MS Intensity Values	sumi
Validation functions	validPeaksMatrix
Find Peak Valleys	valleys
vapply wrappers	vapply1c vapply1d vapply1l
Which is the first/last TRUE value.	which.first which.last

Package: MsCoreUtils 1.25.4

MsCoreUtils: Core Utils for Mass Spectrometry Data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)