Processing and Quantification of Targeted Mass Spectrometry
Imaging Data
![[R logo]](figures/logo.png)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘quantMSImageR’ version 0.99.6
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 |