Introduction | Installation | Mass Spectrometry Feature Grouping | Grouping of features by similar retention time | Grouping of features by abundance correlation across samples | Performing feature grouping on a subset of features | Session information
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:
MsFeatures_1.21.0.tar.gz
MsFeatures_1.21.0.zip(r-4.7)MsFeatures_1.21.0.zip(r-4.6)MsFeatures_1.21.0.zip(r-4.5)
MsFeatures_1.21.0.tgz(r-4.6-any)MsFeatures_1.21.0.tgz(r-4.5-any)
MsFeatures_1.21.0.tar.gz(r-4.7-any)MsFeatures_1.21.0.tar.gz(r-4.6-any)
MsFeatures_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsFeatures/json (API)
| # 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
Last updated from:1ac5d68284. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 187 | ||
| linux-devel-x86_64 | OK | 326 | ||
| source / vignettes | OK | 253 | ||
| linux-release-x86_64 | OK | 272 | ||
| macos-release-arm64 | OK | 173 | ||
| macos-oldrel-arm64 | OK | 149 | ||
| windows-devel | OK | 203 | ||
| windows-release | OK | 180 | ||
| windows-oldrel | OK | 193 | ||
| wasm-release | OK | 157 |
Exports:AbundanceSimilarityParamcorRowsfeatureGroupsfeatureGroups<-groupClosestgroupConsecutivegroupFeaturesgroupSimilarityMatrixSimilarRtimeParam
Dependencies:abindBiobaseBiocGenericsclueclusterDelayedArraygenericsGenomicRangesIRangeslatticeMASSMatrixMatrixGenericsmatrixStatsMsCoreUtilsProtGenericsRcppS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Correlate rows of a numeric matrix | corRows |
| Get or set feature group definitions from an object | featureGroups featureGroups,SummarizedExperiment-method featureGroups<- featureGroups<-,SummarizedExperiment-method |
| Group values with differences below threshold | groupClosest |
| Grouping of sorted values into sets with smallest differences | groupConsecutive |
| General Feature Grouping Concept | groupFeatures |
| Group features based on abundance similarities across samples | AbundanceSimilarityParam groupFeatures,matrix,AbundanceSimilarityParam-method groupFeatures,SummarizedExperiment,AbundanceSimilarityParam-method groupFeatures-similar-abundance |
| Group features based on approximate retention times | groupFeatures,numeric,SimilarRtimeParam-method groupFeatures,SummarizedExperiment,SimilarRtimeParam-method groupFeatures-similar-rtime SimilarRtimeParam |
| Group rows of a diagonal matrix using a threshold | groupSimilarityMatrix |
| Identifies groups with intragroup pairwise distances less than maxDiff | groupSimilarityMatrixTree |
| Quantified LC-MS preprocessing result test data | se |
