Man pages for CeMOS-Mannheim/moleculaR
Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging
| analytePointPattern | analytePointPattern Class Constructor |
| batchAnalyteSearch | Batch Analyte detection in an MSI dataset |
| batchLipidSearch | Batch lipid detection in an MSI dataset |
| createHotspotWin | Create a Hotspot Window for Simulation |
| createSparseMat | Creates a sparse matrix from a list of 'MassPeaks' objects |
| createSpatialWindow | Create Spatial Window of MSI Data |
| dot-bw.scott2 | Calculate Gaussian bandwideth - 'scott' |
| dot-bw.spAutoCorr | Calculate Gaussian bandwidth based on spatial autocorrelation... |
| dot-erosion | Apply erosion to an spp |
| dot-foldChangeNorm | Normalize Intensity based on foldchange |
| dot-getFwhm | Full width half Maximum of peaks |
| dot-getMaxCurve | Maximum curvature |
| dot-isNorm | IS Intensity Normalization |
| dot-kneedle | Find the knee/elbow point in a vector using the Kneedle... |
| dot-medianNorm | Median Intensity Normalization |
| dot-rmsNorm | RMS Intensity Normalization |
| dot-shrinkData | Shrink data |
| dot-ticNorm | TIC Intensity Normalization |
| downloadExData | Download example MSI data |
| dsc | Dice Similarity Coefficient of two window objects |
| estimateFwhm | Estimation of fwhm as a function of m/z axis |
| evalSpatialExpr | Evaluates an expression of SPP objects |
| filterDuplicates | Filtersout duplicated analytes |
| filterPeaks | Filter Peaks |
| focusPlot | Plot a spectrum focusing on a specific mass-range |
| fwhm | fwhm Class Constructor |
| gaussWeight | Gaussian weight as a function of distance and fwhm |
| getFwhm | Get fwhm for a given m/z value |
| im2spp | Convert 'im' to 'anlaytePointPattern' |
| initLipidSearch | Initialize lipids search |
| kneePoint | Find Knee (or elbow) point of a curve |
| lipidSearchList | lipidSearchList Class Constructor |
| loadSwissDB | Load The Swisslipids database |
| manualSpatstatImport | import spatstat sub-packages |
| moleculaR | moleculaR: Spatial Probabilistic Mapping of Metabolite... |
| molProbMap | molProbMap Class Constructor |
| mse | Mean Squared Error |
| ncc | Normalized cross correlation |
| normalizeIntensity | Normalize Intensity |
| plotAnalyte | Plot analytePointPattern |
| plotImg | Plot raster images of type 'im' |
| plot.molProbMap | Plot molecular Probability Maps |
| probMap | Calculate molecular probablity maps |
| readCentrData | Read imzML data |
| readSingleSpect | Read a single spectrum |
| recreateExData | Re-create example data |
| runShiny | Runs one of the campanion shiny apps |
| searchAnalyte | Analyte detection in an MSI dataset |
| searchLipid | Find lipids in MSI datasets |
| simulatespp | Simulate a Spatial Point Pattern |
| sparseIntensityMatrix | sparseIntensityMatrix Class Constructor |
| spp2im | Convert 'anlaytePointPattern' to 'im' |
| subsetAnalytes | Subset analytePointPatterns |
| superImposeAnalytes | Superimpose analytePointPatterns |
| superimposeNoise | Superimpose noise over MSI data |
| transformIntensity | Intensity transformation for SPPs |
| useDefaultFwhm | Use pre-computed default FWHM models |
