Package: quantMSImageR 0.99.0

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:Matthew J. Smith [aut, cre]

quantMSImageR_0.99.0.tar.gz
quantMSImageR_0.99.0.zip(r-4.7-any)quantMSImageR_0.99.0.zip(r-4.6-any)quantMSImageR_0.99.0.zip(r-4.5-any)
quantMSImageR_0.99.0.tgz(r-4.6-any)quantMSImageR_0.99.0.tgz(r-4.5-any)
quantMSImageR_0.99.0.tar.gz(r-4.7-any)quantMSImageR_0.99.0.tar.gz(r-4.6-any)
quantMSImageR_0.99.0.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://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mjs-708/quantmsimager/issues

On CRAN:

Conda:

softwaremassspectrometryimagingmassspectrometrymetabolomicslipidomicsqualitycontrolnormalizationvisualization

3.78 score 38 exports 91 dependencies

Last updated from:8be881d9e2. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING200
linux-devel-x86_64WARNING271
source / vignettesOK327
linux-release-x86_64WARNING265
macos-release-arm64WARNING193
macos-oldrel-arm64WARNING131
windows-devel-x86_64WARNING198
windows-release-x86_64WARNING218
windows-oldrel-x86_64WARNING212
wasm-releaseOK169

Exports:align_featuresapplySNRback2NAbind_panelsbuild_feature_metacalibrationDatacalibrationData<-calibrationDiagnosticscalibrationInfocalibrationLevelscalibrationMetadatacalibrationModelscalibrationModels<-calibrationR2combine_MSIscreate_cal_curvecreateMSIDatamatrixgenerate_txt_imagesimageRint2concint2responseint2snrplot_cal_coveragequant_MSImagingExperimentquant_palettesquantile_hmread_mrmremove_blank_mzsrun_examplerun_studyselect_tissue_pixelssummarise_cal_levelstissueDatatissueInfotissueMatrixtrim_MSIvalidate_configzero2na

Dependencies:base64encBHBiobaseBiocGenericsBiocParallelbslibcachemCardinalCardinalIOchemCalcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondigestdoParalleldplyrevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGetoptLongggplot2GlobalOptionsgluegridExtragtablehighrhtmltoolsIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMatrixmatrixStatsmattermemoisemimenlmeontologyIndexpatchworkpillarpkgconfigpngpracmaProtGenericspurrrR6rappdirsRColorBrewerrjsonrlangrmarkdownS4VectorsS7sassscalesshapesnowstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

Introduction to quantMSImageR
Introduction | What this package does | Scope | The workflow | Installation | Quick start | The data model | Reading your own data | Loading the acquisitions | Selecting tissue pixels | Ion images | Colour-scale treatment | Quantile heatmaps across samples | Signal-to-noise filtering | Running a full study from a YAML config | The configuration as a record of the analysis | References | Session information
Rendered fromquantMSImageR.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
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 | R² is not enough | 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
Rendered fromquantification.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-20

Readme and manuals

Help Manual

Help pageTopics
Align two MSI objects to their common featuresalign_features
Apply SNR mask to intensity valuesapplySNR applySNR,quant_MSImagingExperiment-method
Set background pixel intensities to NAback2NA back2NA,quant_MSImagingExperiment-method
Merge two MSI objects of the same tissue by coordinate-matched rbindbind_panels
Build per-feature metadata by joining an ion library on m/zbuild_feature_meta
Calibration metadata for an imaging experimentcalibrationInfo calibrationInfo-class
Combine MSI experiments across acquisitionscombine_MSIs combine_MSIs,MSImagingExperiment-method
Fit per-analyte calibration modelscreate_cal_curve create_cal_curve,quant_MSImagingExperiment-method
Create a feature-by-sample MSI data matrixcreateMSIDatamatrix createMSIDatamatrix,quant_MSImagingExperiment-method
Load, process and optionally export per-feature text-image matricesgenerate_txt_images
Draw an ion image for one featureimageR imageR,quant_MSImagingExperiment-method
Convert response to calibrated amount estimatesint2conc int2conc,quant_MSImagingExperiment-method
Normalise pixel intensities to internal-standard responseint2response int2response,quant_MSImagingExperiment-method
Calculate background-referenced signal-to-noise ratiosint2snr int2snr,quant_MSImagingExperiment-method
Check that measured pixels fall within the calibrated rangeplot_cal_coverage plot_cal_coverage,quant_MSImagingExperiment-method
Print a validation resultprint.quant_validation
Quantifiable MS imaging experimentquant_MSImagingExperiment quant_MSImagingExperiment-class
Colour palettes used by quantMSImageRquant_palettes
Quantile heatmap of MSI features across samplesquantile_hm
Accessors for calibration and tissue metadatacalibrationData 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
Read a Waters DESI-MRM acquisition into an MSImagingExperimentread_mrm
Remove features without observed signalremove_blank_mzs remove_blank_mzs,quant_MSImagingExperiment-method
Run the quantMSImageR example studyrun_example
Run a full DESI-MRM study from a YAML configurationrun_study
Interactively select tissue pixels for an acquisitionselect_tissue_pixels
Summarise the response at each calibration levelsummarise_cal_levels summarise_cal_levels,quant_MSImagingExperiment-method
Tissue-level summaries for an imaging experimenttissueInfo tissueInfo-class
Remove pure-background border rows and columns from an MSI objecttrim_MSI
Validate a study YAML configurationvalidate_config
Replace zero intensities with NAzero2na zero2na,quant_MSImagingExperiment-method