msi.dataset-class

<a rd-options="" href="/link/msi.dataset-class?package=SPUTNIK&version=1.3.3" data-mini-rdoc="SPUTNIK::msi.dataset-class">msi.dataset-class</a> S4 class definition containing the information about
the mass spectrometry imaging dataset.

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.

Paolo Inglese

SPUTNIK

SPatially aUTomatic deNoising for Ims toolKit

Goncalo Correia

msi.dataset-class function

<dl class="dl-horizontal">
<dt><code>matrix</code></dt><dd>the peaks intensity matrix. Rows represent pixels, and columns
represent peaks.</dd></dl><dt><code>mz</code></dt><dd>vector of matched m/z values.</dd><dt><code>nrow</code></dt><dd>geometrical shape (number of rows) of image.</dd><dt><code>ncol</code></dt><dd>geometrical shape (number of columns) of image.</dd><dt><code>norm</code></dt><dd>normalization method</dd><dt><code>normoffset</code></dt><dd>numeric offset used for the normalization</dd><dt><code>vartr</code></dt><dd>variance stabilizing transformation</dd><dt><code>vartroffset</code></dt><dd>numeric offset used for the variance stabilizing transformation</dd>

Slots

<a rd-options='' href='msi.dataset-class'>msi.dataset-class</a> S4 class definition containing the information about
the mass spectrometry imaging dataset.

<a rd-options='' href='msi.dataset-class'>msi.dataset-class</a> S4 class definition containing the information about
the mass spectrometry imaging dataset. — msi.dataset-class

<a rd-options='' href='msi.dataset-class'>msi.dataset-class</a> S4 class definition containing the information about
the mass spectrometry imaging dataset.

<a rd-options="" href="/link/msi.dataset-class?package=SPUTNIK&version=1.3.3" data-mini-rdoc="SPUTNIK::msi.dataset-class">msi.dataset-class</a> S4 class definition containing the information about
the mass spectrometry imaging dataset.

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

Description

Arguments

Slots