Data_testclust


To test for the best unsupervised clustering method, a dataset where molecules are already identified is created.  Each molecule is represented by several samples mass spectrum. Here, the dataset contains 10 molecules obtained in different samples (84 Lavandula GC-MS analyses). In the function MS.test.clust, different clustering methods are tested for their abilities to find the correct structure of the dataset. Three different cluster validity indices are calculated to evaluate the results: the matching coefficient, the silhouette width and the Dunn index (see MS.test.clust for details)

datasets

Package for the detection of molecules in complex mixtures
of compounds. It creates an initial_DATA matrix from several
GC-MS analyses by collecting and assembling the information
from chromatograms and mass spectra (MS.DataCreation), It can
read several format (ASCII, CDF, mzML, mzXML or mzData).It
tests for the best unsupervised clustering method to group
similar mass spectra into molecules (MS.test.clust).It runs the
optimal unsupervised clustering method on the initial_DATA
matrix, identifies the optimal number of clusters, produces
different files for facilitating the quality control and
identification of putative molecules, and returns
fingerprinting or profiling matrices (MS.clust).It converts
output files from MS.clust for NIST mass spectral library
search and ARISTO webtool search

Yann Guitton

MSeasy

Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS)
data

Data_testclust function

A data frame with 10 molecules from 84 GC-MS analyses.
  <ul>
<li><code>header line  </code>  the first row must contains the columns' names
    </li>
<li><code>first column </code> name of the molecule  
    </li>
<li><code>second column </code> sample name  
    </li>
<li><code>third column </code> retention time  
    </li>
<li><code>following columns </code> mean relative mass spectrum of the molecule (the intensity of one mass fragment (m/z) per column; Mean mass spectrum calculated by averaging 5 percent of the mass spectra surrounding the apex; The intensity of each mass fragment is transformed to a relative percentage of the highest mass fragment per spectrum)
</li>
</ul> 

Data_testclust: Demonstration dataset for MS.test.clust

Description

Usage

Arguments

Format

Examples