SPatially aUTomatic deNoising for Ims toolKit

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.


News

ChangeLog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.2] - 2019-04-16

Fixed

  • Now imager::threshold is called with approximate=FALSE in the scatter.ratio function to use all ion image pixels

[1.1.1] - 2018-10-25

Fixed

  • Fixed bug in the global reference filter that won't allow the calculation of the similarity measures when constant columns are present in the intensity matrix.

[1.1] - 2018-10-19

Added

  • New ROI detection using linear SVM. The user must select representative regions of the off-sample and sample-related areas. Then, a linear SVM performs the segmentation of the data, generating the ROI.
  • New ROI detection using k-means with a larger number of clusters than 2. This allows a finer detection of the sample-related region.
  • Now the covariate image for the Kolmogorov-Smirnov test can be passed as argument of the function 'CSRPeaksFilter' (see doc).
  • New functions 'addBorderImage' and 'remBorderImage' to add or remove a border of N pixels from an MS image.

Fixed

  • Fixed the SSIM function (it does not require scaling)
  • Fixed typos in the help

[1.0.4.1] - 2018-10-08

Removed

  • Removed dependency from 'autothresholdr' package. Now Otsu is performed using the function threshold(x, 'auto') from 'imager'.

[1.0.4] - 2018-10-06

Fixed

  • Fixed a bug in the function .match.mz.array.
  • Improved the comments in the function .match.mz.array.

Reference manual

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install.packages("SPUTNIK")

1.1.2 by Paolo Inglese, 8 months ago


https://github.com/paoloinglese/SPUTNIK


Report a bug at https://github.com/paoloinglese/SPUTNIK/issues


Browse source code at https://github.com/cran/SPUTNIK


Authors: Paolo Inglese [aut, cre] , Goncalo Correia [aut, ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports e1071, spatstat, viridis, SDMTools, ggplot2, reshape, imager, methods, infotheo, parallel


See at CRAN