Introduction | What this package does | Scope | The workflow | Installation | Quick start | The data model | Reading your own data | Loading the acquisitions | Pieces of one tissue | Selecting tissue pixels | Labelling regions of interest | What the labels look like downstream | Ion images | Colour-scale treatment | Quantile heatmaps across samples | Seeing which sample carried a group effect | Signal-to-noise filtering | Running a full study from a YAML config | Samples made of several acquisitions | Comparing regions of interest | The configuration as a record of the analysis | References | Session information
Package: quantMSImageR 0.99.9
Matthew J. Smith
quantMSImageR: Processing and Quantification of Targeted Mass Spectrometry Imaging Data
Implements tools for processing and quantifying targeted DESI-MRM mass spectrometry imaging (MSI) datasets, extending the Cardinal package. Includes signal-to-noise filtering against background pixels, tissue/background separation, per-feature ion images, quantile heatmaps, quantification against on-slide or on-tissue calibration standards, and batch export of per-feature text images for external viewers.
Authors:
quantMSImageR_0.99.9.tar.gz
quantMSImageR_0.99.9.zip(r-4.7-any)quantMSImageR_0.99.9.zip(r-4.6-any)quantMSImageR_0.99.9.zip(r-4.5-any)
quantMSImageR_0.99.9.tgz(r-4.6-any)quantMSImageR_0.99.9.tgz(r-4.5-any)
quantMSImageR_0.99.9.tar.gz(r-4.7-any)quantMSImageR_0.99.9.tar.gz(r-4.6-any)
quantMSImageR_0.99.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
quantMSImageR/json (API)
| # Install 'quantMSImageR' in R: |
| install.packages('quantMSImageR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mjs-708/quantmsimager/issues
On BioConductor:quantMSImageR-0.99.8(bioc 3.24)
softwaremassspectrometryimagingmassspectrometrymetabolomicslipidomicsqualitycontrolnormalizationvisualization
Last updated from:14e7384b88. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 198 | ||
| linux-devel | OK | 373 | ||
| source / vignettes | OK | 289 | ||
| linux-release | OK | 367 | ||
| macos-release | OK | 209 | ||
| macos-oldrel | OK | 180 | ||
| windows-devel | OK | 225 | ||
| windows-release | OK | 236 | ||
| windows-oldrel | OK | 220 | ||
| wasm-release | OK | 175 |
Exports:alignFeaturesapplySNRback2NAbindPanelsbuildFeatureMetacalibrationDatacalibrationData<-calibrationDiagnosticscalibrationInfocalibrationLevelscalibrationMetadatacalibrationModelscalibrationModels<-calibrationR2combineMSIscontributionHmcreateCalCurvecreateMSIDataMatrixgenerateTxtImagesimageRint2concint2responseint2SNRlabelROIsplotCalCoveragequant_MSImagingExperimentquantileHmquantPalettesreadMRMremoveBlankMzsrunExamplerunStudyselectTissuePixelsshowstitchAcquisitionssummariseCalLevelstissueDatatissueInfotissueMatrixtrimMSIvalidateConfigzero2NA
Dependencies:base64encBHBiobaseBiocGenericsBiocParallelbslibcachemCardinalCardinalIOchemCalcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondigestdoParalleldplyrevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGetoptLongggplot2GlobalOptionsgluegridExtragtablehighrhtmltoolsIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMatrixmatrixStatsmattermemoisemimenlmeontologyIndexpatchworkpillarpkgconfigpngpracmaProtGenericspurrrR6rappdirsRColorBrewerrjsonrlangrmarkdownS4VectorsS7sassscalesshapesnowstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml
Introduction to quantMSImageR
Last update: 2026-09-23
Started: 2026-07-20
Quantification with calibration standards
Introduction | On-slide versus on-tissue calibration | Scope and assumptions | Installation | Calibration workflow overview | The bundled calibration dataset | Fitting and diagnosing calibration models | Applying the models to a study section | Checking calibration coverage | Handling out-of-range pixels | Driving calibration from a study YAML | Interpretation and limitations | References | Session information
Last update: 2026-08-20
Started: 2026-07-20
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align two MSI objects to their common features | alignFeatures |
| Apply SNR mask to intensity values | applySNR applySNR,quant_MSImagingExperiment-method |
| Set background pixel intensities to NA | back2NA back2NA,quant_MSImagingExperiment-method |
| Merge two MSI objects of the same tissue by coordinate-matched rbind | bindPanels |
| Build per-feature metadata by joining an ion library on m/z | buildFeatureMeta |
| Calibration metadata for an imaging experiment | calibrationInfo calibrationInfo-class show,calibrationInfo-method |
| Combine MSI experiments across acquisitions | combineMSIs combineMSIs,MSImagingExperiment-method |
| Group-mean heatmap with per-sample contribution as opacity | contributionHm |
| Fit per-analyte calibration models | createCalCurve createCalCurve,quant_MSImagingExperiment-method |
| Create a feature-by-sample MSI data matrix | createMSIDataMatrix createMSIDataMatrix,quant_MSImagingExperiment-method |
| Load, process and optionally export per-feature text-image matrices | generateTxtImages |
| Draw an ion image for one feature | imageR imageR,quant_MSImagingExperiment-method |
| Convert response to calibrated amount estimates | int2conc int2conc,quant_MSImagingExperiment-method |
| Normalise pixel intensities to internal-standard response | int2response int2response,quant_MSImagingExperiment-method |
| Calculate background-referenced signal-to-noise ratios | int2SNR int2SNR,quant_MSImagingExperiment-method |
| Label regions of interest within the tissue of an acquisition | labelROIs |
| Check that measured pixels fall within the calibrated range | plotCalCoverage plotCalCoverage,quant_MSImagingExperiment-method |
| Print a validation result | print.quantValidation |
| Quantifiable MS imaging experiment | quant_MSImagingExperiment quant_MSImagingExperiment-class |
| Quantile heatmap of MSI features across samples | quantileHm |
| Accessors for calibration and tissue metadata | calibrationData calibrationData,quant_MSImagingExperiment-method calibrationData<- calibrationData<-,quant_MSImagingExperiment-method calibrationDiagnostics calibrationDiagnostics,quant_MSImagingExperiment-method calibrationLevels calibrationLevels,quant_MSImagingExperiment-method calibrationMetadata calibrationMetadata,quant_MSImagingExperiment-method calibrationModels calibrationModels,quant_MSImagingExperiment-method calibrationModels<- calibrationModels<-,quant_MSImagingExperiment-method calibrationR2 calibrationR2,quant_MSImagingExperiment-method quantMSImageR-accessors tissueData tissueData,quant_MSImagingExperiment-method tissueMatrix tissueMatrix,quant_MSImagingExperiment-method |
| Colour palettes used by quantMSImageR | quantPalettes |
| Read a Waters DESI-MRM acquisition into an MSImagingExperiment | readMRM |
| Remove features without observed signal | removeBlankMzs removeBlankMzs,quant_MSImagingExperiment-method |
| Run the quantMSImageR example study | runExample |
| Run a full DESI-MRM study from a YAML configuration | runStudy |
| Interactively select tissue pixels for an acquisition | selectTissuePixels |
| Stitch acquisitions that are pieces of one tissue into a single sample | stitchAcquisitions |
| Summarise the response at each calibration level | summariseCalLevels summariseCalLevels,quant_MSImagingExperiment-method |
| Tissue-level summaries for an imaging experiment | show,tissueInfo-method tissueInfo tissueInfo-class |
| Remove pure-background border rows and columns from an MSI object | trimMSI |
| Validate a study YAML configuration | validateConfig |
| Replace zero intensities with NA | zero2NA zero2NA,quant_MSImagingExperiment-method |