R: Processing and Quantification of Targeted Mass Spectrometry Imaging Data

# Processing and Quantification of Targeted Mass Spectrometry Imaging Data

## Documentation for package ‘quantMSImageR’ version 0.99.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

alignFeatures | Align two MSI objects to their common features
applySNR | Apply SNR mask to intensity values
applySNR-method | Apply SNR mask to intensity values
back2NA | Set background pixel intensities to NA
back2NA-method | Set background pixel intensities to NA
bindPanels | Merge two MSI objects of the same tissue by coordinate-matched rbind
buildFeatureMeta | Build per-feature metadata by joining an ion library on m/z
calibrationData | Accessors for calibration and tissue metadata
calibrationData-method | Accessors for calibration and tissue metadata
calibrationData<- | Accessors for calibration and tissue metadata
calibrationData<--method | Accessors for calibration and tissue metadata
calibrationDiagnostics | Accessors for calibration and tissue metadata
calibrationDiagnostics-method | Accessors for calibration and tissue metadata
calibrationInfo | Calibration metadata for an imaging experiment
calibrationInfo-class | Calibration metadata for an imaging experiment
calibrationLevels | Accessors for calibration and tissue metadata
calibrationLevels-method | Accessors for calibration and tissue metadata
calibrationMetadata | Accessors for calibration and tissue metadata
calibrationMetadata-method | Accessors for calibration and tissue metadata
calibrationModels | Accessors for calibration and tissue metadata
calibrationModels-method | Accessors for calibration and tissue metadata
calibrationModels<- | Accessors for calibration and tissue metadata
calibrationModels<--method | Accessors for calibration and tissue metadata
calibrationR2 | Accessors for calibration and tissue metadata
calibrationR2-method | Accessors for calibration and tissue metadata
combineMSIs | Combine MSI experiments across acquisitions
combineMSIs-method | Combine MSI experiments across acquisitions
contributionHm | Group-mean heatmap with per-sample contribution as opacity
createCalCurve | Fit per-analyte calibration models
createCalCurve-method | Fit per-analyte calibration models
createMSIDataMatrix | Create a feature-by-sample MSI data matrix
createMSIDataMatrix-method | Create a feature-by-sample MSI data matrix
generateTxtImages | Load, process and optionally export per-feature text-image matrices
imageR | Draw an ion image for one feature
imageR-method | Draw an ion image for one feature
int2conc | Convert response to calibrated amount estimates
int2conc-method | Convert response to calibrated amount estimates
int2response | Normalise pixel intensities to internal-standard response
int2response-method | Normalise pixel intensities to internal-standard response
int2SNR | Calculate background-referenced signal-to-noise ratios
int2SNR-method | Calculate background-referenced signal-to-noise ratios
plotCalCoverage | Check that measured pixels fall within the calibrated range
plotCalCoverage-method | Check that measured pixels fall within the calibrated range
print.quantValidation | Print a validation result
quantileHm | Quantile heatmap of MSI features across samples
quantMSImageR-accessors | Accessors for calibration and tissue metadata
quantPalettes | Colour palettes used by quantMSImageR
quant_MSImagingExperiment | Quantifiable MS imaging experiment
quant_MSImagingExperiment-class | Quantifiable MS imaging experiment
readMRM | Read a Waters DESI-MRM acquisition into an MSImagingExperiment
removeBlankMzs | Remove features without observed signal
removeBlankMzs-method | Remove features without observed signal
runExample | Run the quantMSImageR example study
runStudy | Run a full DESI-MRM study from a YAML configuration
selectTissuePixels | Interactively select tissue pixels for an acquisition
show-method | Calibration metadata for an imaging experiment
show-method | Tissue-level summaries for an imaging experiment
stitchAcquisitions | Stitch acquisitions that are pieces of one tissue into a single sample
summariseCalLevels | Summarise the response at each calibration level
summariseCalLevels-method | Summarise the response at each calibration level
tissueData | Accessors for calibration and tissue metadata
tissueData-method | Accessors for calibration and tissue metadata
tissueInfo | Tissue-level summaries for an imaging experiment
tissueInfo-class | Tissue-level summaries for an imaging experiment
tissueMatrix | Accessors for calibration and tissue metadata
tissueMatrix-method | Accessors for calibration and tissue metadata
trimMSI | Remove pure-background border rows and columns from an MSI object
validateConfig | Validate a study YAML configuration
zero2NA | Replace zero intensities with NA
zero2NA-method | Replace zero intensities with NA