Package: MsFeatures 1.21.0

Johannes Rainer

MsFeatures: Functionality for Mass Spectrometry Features

The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.

Authors:Johannes Rainer [aut, cre], Johan Lassen [ctb]

MsFeatures_1.21.0.tar.gz
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MsFeatures_1.21.0.tgz(r-4.6-any)MsFeatures_1.21.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
MsFeatures/json (API)
NEWS

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

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

Datasets:
  • se - Quantified LC-MS preprocessing result test data

On BioConductor:MsFeatures-1.21.0(bioc 3.24)MsFeatures-1.20.0(bioc 3.23)

infrastructuremassspectrometrymetabolomics

8.37 score 7 stars 15 packages 51 scripts 2.4k downloads 9 exports 23 dependencies

Last updated from:1ac5d68284. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING153
linux-devel-x86_64OK249
source / vignettesOK224
linux-release-x86_64OK258
macos-release-arm64OK180
macos-oldrel-arm64OK168
windows-develOK174
windows-releaseOK174
windows-oldrelOK148
wasm-releaseOK115

Exports:AbundanceSimilarityParamcorRowsfeatureGroupsfeatureGroups<-groupClosestgroupConsecutivegroupFeaturesgroupSimilarityMatrixSimilarRtimeParam

Dependencies:abindBiobaseBiocGenericsclueclusterDelayedArraygenericsGenomicRangesIRangeslatticeMASSMatrixMatrixGenericsmatrixStatsMsCoreUtilsProtGenericsRcppS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

Grouping Mass Spectrometry Features

Rendered fromMsFeatures.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-01-25
Started: 2021-01-25

Readme and manuals

Help Manual

Help pageTopics
Correlate rows of a numeric matrixcorRows
Get or set feature group definitions from an objectfeatureGroups featureGroups,SummarizedExperiment-method featureGroups<- featureGroups<-,SummarizedExperiment-method
Group values with differences below thresholdgroupClosest
Grouping of sorted values into sets with smallest differencesgroupConsecutive
General Feature Grouping ConceptgroupFeatures
Group features based on abundance similarities across samplesAbundanceSimilarityParam groupFeatures,matrix,AbundanceSimilarityParam-method groupFeatures,SummarizedExperiment,AbundanceSimilarityParam-method groupFeatures-similar-abundance
Group features based on approximate retention timesgroupFeatures,numeric,SimilarRtimeParam-method groupFeatures,SummarizedExperiment,SimilarRtimeParam-method groupFeatures-similar-rtime SimilarRtimeParam
Group rows of a diagonal matrix using a thresholdgroupSimilarityMatrix
Identifies groups with intragroup pairwise distances less than maxDiffgroupSimilarityMatrixTree
Quantified LC-MS preprocessing result test datase