Introduction | Installation | Getting data | Mass spectrometry experiment | Experiment files | Experimental design | Raw data | Third party applications | Saving and reusing experiments | Linking experimental data to samples | Subset and filter MsExperiment | Using MsExperiment with MsBackendSql | Session information
Package: MsExperiment 1.15.0
Laurent Gatto
MsExperiment: Infrastructure for Mass Spectrometry Experiments
Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.
Authors:
MsExperiment_1.15.0.tar.gz
MsExperiment_1.15.0.zip(r-4.7)MsExperiment_1.15.0.zip(r-4.6)MsExperiment_1.15.0.zip(r-4.5)
MsExperiment_1.15.0.tgz(r-4.6-any)MsExperiment_1.15.0.tgz(r-4.5-any)
MsExperiment_1.15.0.tar.gz(r-4.7-any)MsExperiment_1.15.0.tar.gz(r-4.6-any)
MsExperiment_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsExperiment/json (API)
| # Install 'MsExperiment' in R: |
| install.packages('MsExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rformassspectrometry/msexperiment/issues
On BioConductor:MsExperiment-1.15.0(bioc 3.24)MsExperiment-1.14.0(bioc 3.23)
infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport
Last updated from:e608756e18. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 212 | ||
| linux-devel-x86_64 | NOTE | 487 | ||
| source / vignettes | OK | 353 | ||
| linux-release-x86_64 | NOTE | 407 | ||
| macos-release-arm64 | NOTE | 207 | ||
| macos-oldrel-arm64 | NOTE | 326 | ||
| windows-devel | NOTE | 421 | ||
| windows-release | NOTE | 471 | ||
| windows-oldrel | NOTE | 472 | ||
| wasm-release | OK | 205 |
Exports:dbWriteSampleDataexistMsExperimentFilesexperimentFilesexperimentFiles<-filterSpectralinkSampleDataMsExperimentMsExperimentFilesotherDataotherData<-qdataqdata<-readMsExperimentsampleDatasampleData<-showspectraspectra<-spectraSampleIndex
Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Write sample annotations to a MsBackendSql SQL database | dbWriteSampleData |
| Managing Mass Spectrometry Experiments | experimentFiles experimentFiles<- filterSpectra,MsExperiment,function-method length,MsExperiment-method linkSampleData MsExperiment MsExperiment-class otherData otherData<- qdata qdata<- sampleData sampleData<- show,MsExperiment-method spectra,MsExperiment-method spectra<-,MsExperiment-method spectraSampleIndex [,MsExperiment,ANY,ANY,ANY-method |
| A class to store experiment files | existMsExperimentFiles MsExperimentFiles MsExperimentFiles-class show,MsExperimentFiles-method |
| Import MS spectra data of an experiment | readMsExperiment |
