Package: MsCoreUtils 1.19.0

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], 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]

MsCoreUtils_1.19.0.tar.gz
MsCoreUtils_1.19.0.zip(r-4.5)MsCoreUtils_1.19.0.zip(r-4.4)MsCoreUtils_1.19.0.zip(r-4.3)
MsCoreUtils_1.19.0.tgz(r-4.4-x86_64)MsCoreUtils_1.19.0.tgz(r-4.4-arm64)MsCoreUtils_1.19.0.tgz(r-4.3-x86_64)MsCoreUtils_1.19.0.tgz(r-4.3-arm64)
MsCoreUtils_1.19.0.tar.gz(r-4.5-noble)MsCoreUtils_1.19.0.tar.gz(r-4.4-noble)
MsCoreUtils_1.19.0.tgz(r-4.4-emscripten)MsCoreUtils_1.19.0.tgz(r-4.3-emscripten)
MsCoreUtils.pdf |MsCoreUtils.html✨
MsCoreUtils/json (API)
NEWS

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

Peer review:

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

On BioConductor:MsCoreUtils-1.19.0(bioc 3.21)MsCoreUtils-1.18.0(bioc 3.20)

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils

10.66 score 16 stars 67 packages 40 scripts 5.9k downloads 74 exports 7 dependencies

Last updated 24 days agofrom:6a5c06dfdb. Checks:OK: 7 ERROR: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-win-x86_64NOTENov 03 2024
R-4.5-linux-x86_64ERRORNov 21 2024
R-4.4-win-x86_64OKNov 03 2024
R-4.4-mac-x86_64OKNov 03 2024
R-4.4-mac-aarch64OKNov 03 2024
R-4.3-win-x86_64OKNov 03 2024
R-4.3-mac-x86_64OKNov 03 2024
R-4.3-mac-aarch64OKNov 03 2024

Exports:%between%aggregate_by_matrixaggregate_by_vectorasIntegerbetweenbinbreaks_ppmclosestcoefMAcoefSGcoefWMAcolCountscolMeansMatcolSumsMatcommoncommon_pathentropyestimateBaselineestimateBaselineConvexHullestimateBaselineMedianestimateBaselineSnipestimateBaselineTopHatforce_sortedformatRtgetImputeMargingnpsgroupi2indeximpute_bpcaimpute_funimpute_knnimpute_matriximpute_minimpute_MinDetimpute_MinProbimpute_mixedimpute_mleimpute_neighbour_averageimpute_QRILCimpute_RFimpute_withimpute_zeroimputeMethodsisPeaksMatrixjoinjoin_gnpslocalMaximamaximedianPolishnavdistndotproductnentropyneuclideannoisenormalize_matrixnormalizeMethodsnspectraangleppmrbindFillrefineCentroidsrlarobustSummaryrowRlart2characterrt2numericsmoothsumivalidPeaksMatrixvalleysvapply1cvapply1dvapply1lwhich.firstwhich.last

Dependencies:BiocGenericsclueclustergenericsMASSRcppS4Vectors

Core Utils for Mass Spectrometry Data

MsCoreUtils Package Maintainers

Rendered fromMsCoreUtils.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2022-02-18
Started: 2020-04-05

Readme and manuals

Help Manual

Help pageTopics
Aggreagate quantitative featuresaggregate aggregate_by_matrix aggregate_by_vector colMeansMat colSumsMat
Range helper functions%between% between
Binningbin
Sequence with increasing difference between elementsbreaks_ppm
Relaxed Value Matchingclosest common join
Coerce functionsasInteger coerce
Counts the number of featurescolCounts
Extract the common file pathcommon_path
Spectra Distance/Similarity Measurementsdistance dotproduct navdist ndotproduct neuclidean nspectraangle
Spectral entropyentropy nentropy
Estimates the Baseline of a Mass SpectrumestimateBaseline estimateBaselineConvexHull estimateBaselineMedian estimateBaselineSnip estimateBaselineTopHat
Forcing a numeric vector into a monotonously increasing sequence.force_sorted
GNPS spectrum similarity scoresgnps join_gnps
Grouping of numeric values by similaritygroup
Input parameter check for subsetting operationsi2index
Quantitative mass spectrometry data imputationgetImputeMargin 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 functionsisPeaksMatrix
Local MaximalocalMaxima
Maximum MS Intensity Valuemaxi
Return the Median Polish (Robust Twoway Decomposition) of a matrixmedianPolish
Noise Estimationnoise
Quantitative data normalisationnormalizeMethods normalize_matrix
PPM - Parts per Millionppm
Combine R Objects by RowrbindFill
Refine Peak CentroidsrefineCentroids
Calculate relative log abundancesrla rowRla
Return the Robust Expression Summary of a matrixrobustSummary
Format Retention TimeformatRt rt2character rt2numeric
SmoothingcoefMA coefSG coefWMA smooth
Summing MS Intensity Valuessumi
Validation functionsvalidPeaksMatrix
Find Peak Valleysvalleys
vapply wrappersvapply1c vapply1d vapply1l
Which is the first/last TRUE value.which.first which.last