Man pages for SPUTNIK
Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit
| applyPeaksFilter-msi.dataset-method | Apply the results of a peaks filter. |
| binKmeans2-msi.dataset-method | Return a binary mask generated applying k-means clustering on... |
| binKmeans-msi.dataset-method | Return a binary mask generated applying k-means clustering on... |
| binOtsu-ms.image-method | Binarize MS image using Otsu's thresholding. |
| binSupervised-msi.dataset-method | Return a binary mask generated applying a supervised... |
| bladderMALDIRompp2010 | Load the example MALDI-MSI data. |
| closeImage-ms.image-method | Apply morphological closing to binary image. |
| countPixelsFilter | Filter based on the minimum number of connected pixels in the... |
| createPeaksFilter | Generate a peak filter object. |
| CSRPeaksFilter | Performs the peak selection based on complete spatial... |
| getIntensityMat-msi.dataset-method | Return the peaks intensity matrix. |
| getMZ-msi.dataset-method | Return the m/z vector. |
| getShapeMSI-msi.dataset-method | Returns the geometrical shape of MSI dataset |
| gini.index | Gini index. |
| globalPeaksFilter | Reference similarity based peak selection. |
| invertImage-ms.image-method | Invert the colors of an MS image. |
| msiDataset | Constructor for msi.dataset-class objects. |
| msi.dataset-class | msi.dataset-class S4 class definition containing the... |
| msImage | Constructor for ms.image-class objects. |
| ms.image-class | ms.image-class definition. |
| NMI | Normalized mutual information (NMI). |
| normIntensity-msi.dataset-method | Normalize the peaks intensities. |
| numDetectedMSI-msi.dataset-method | Generates an msImage representing the number of detected... |
| ovarianDESIDoria2016 | Load the example DESI-MSI data. |
| PCAImage-msi.dataset-method | Generates an RGB msImage representing the first 3 principal... |
| plot | Visualize an MS image. 'plot' extends the generic function to... |
| refImageBinaryKmeans | Calculate the binary reference image using k-means... |
| refImageBinaryKmeansMulti | Calculate the binary reference image using k-means clustering... |
| refImageBinaryOtsu | Calculate the binary reference image using Otsu's... |
| refImageBinarySVM | Calculate the binary reference image using linear SVM trained... |
| refImageContinuous | 'refImageContinuous' returns the reference image, calculated... |
| removeSmallObjects-ms.image-method | Remove binary ROI objects smaller than user-defined number of... |
| scatter.ratio | Pixel scatteredness ratio. |
| smoothImage-ms.image-method | Apply Gaussian smoothing to an MS image. |
| spatial.chaos | Spatial chaos measure. |
| splitPeaksFilter | Test for the presence of split peaks. |
| SSIM | Structural similarity index (SSIM). |
| totalIonCountMSI-msi.dataset-method | Generates an msImage representing pixels total-ion-counts.... |
| varTransform-msi.dataset-method | Variance stabilizing transformation. |
