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SPUTNIK (version 1.1)

SPatially aUTomatic deNoising for Ims toolKit

Description

A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.

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Install

install.packages('SPUTNIK')

Monthly Downloads

347

Version

1.1

License

GPL (>= 3)

Issues

0

Pull Requests

0

Stars

4

Forks

3

Maintainer

Paolo Inglese

Last Published

October 23rd, 2018

Functions in SPUTNIK (1.1)

applyPeaksFilter,msi.dataset-method

Apply the results of a peaks filter.
normIntensity,msi.dataset-method

Normalize the peaks intensities.
plot,ms.image,missing-method

Visualize an MS image. plot extends the generic function to ms.image-class objects.
countPixelsFilter

Filter based on the minimum number of connected pixels in the ROI.
createPeaksFilter

Generate a peak filter object.
refAndROIimages

Compute the reference image and the ROI mask.
msi.dataset-class

msi.dataset-class S4 class definition containing the information about the mass spectrometry imaging dataset.
ms.image-class

ms.image-class definition.
msImage

Constructor for ms.image-class objects.
msiDataset

Constructor for msi.dataset-class objects.
getIntensityMat,msi.dataset-method

Return the peaks intensity matrix.
getMZ,msi.dataset-method

Return the m/z vector.
removeSmallObjects,ms.image-method

Remove binary ROI objects smaller than user-defined number of pixels
getShapeMSI,msi.dataset-method

Returns the geometrical shape of MS image
gini.index

Gini index.
scatter.ratio

Pixel scatteredness ratio.
globalPeaksFilter

Reference similarity based peak selection.
invertImage,ms.image-method

Invert the colors of an MS image.
smoothImage,ms.image-method

Apply Gaussian smoothing to an MS image.
spatial.chaos

Spatial chaos measure.
ovarianDESIDoria2016

Load the example DESI-MSI data.
splitPeaksFilter

Test for the presence of split peaks.
varTransform,msi.dataset-method

Variance stabilizing transformation.
NMI

Normalized mutual information (NMI).
CSRPeaksFilter

Performs the peak selection based on complete spatial randomness test.
binOtsu,ms.image-method

Binarize MS image using Otsu's thresholding.
binSupervised,msi.dataset-method

Return a binary mask generated applying a supervised classifier on peaks intensities using manually selected regions corresponding to off-sample and sample-related areas.
SSIM

Structural similarity index (SSIM).
binKmeans,msi.dataset-method

Return a binary mask generated applying k-means clustering on peaks intensities.
bladderMALDIRompp2010

Load the example MALDI-MSI data.
closeImage,ms.image-method

Apply morphological closing to binary image.
binKmeans2,msi.dataset-method

Return a binary mask generated applying k-means clustering on peaks intensities. A finer segmentation is obtained by using a larger number of clusters than 2. The off-sample clusters are merged looking at the most frequent labels in the image corners. The lookup areas are defined by the kernel size.