Import data

Data

Networks can be created from a data file (in mgf or msp format) using the Import Data Import Data icon. This will open the following dialog:

Process File Dialog

This dialog lets you open a data file and, optionally, a metadata table (csv file) using the Browse buttons. Separator for the csv file should be auto-detected but you can change this parameter directly in this dialog and more parameters are available via the Options button. See Metadata}.

Parameters used by MetGem for the cosine computations step can be tuned in the Cosine Score Computing section. See Cosine-score computations.

In the Add Views section, you can optionally add visualisations like Molecular Network or 2-D projections. See Add visualisations.

When you have loaded an data file and you are satisfied with the parameters, you can click OK to start the process.

Add visualisations

MetGem offers two types of views that you can add to your project. See Network views.

To add a view, use the dropdown menu next to the add-view button. Choose the desired visualisation and a dialog will open to let you set a few parameters. See Parameters for for more informations about the parameters.

Example of a add visualisation dialog

Metadata

You can associate metadata to the spectra loaded during Data Import data step. You can load these metadata from a csv or from a spreadsheet file (like LibreOffice Calc or Microsoft Excel) or want to load new metadata, you can do so using the Import Metadata tool button from the File Toolbar. The following dialog will pop-up:

Import Metadata Dialog

Metadata file (csv) can be selected using the Browse button. Separator for csv file should be auto-detected but can this be changed in the Options section. More parameters like whether the file contains headers or not can be also be tuned in this section.

You can see the first 100 lines that will be imported in the Preview section. You can select which column to import by clicking on the corresponding headers or via the upper toolbar. If no column is selected, all columns will be imported.

The Refresh button can be used to reload file from disk using the parameters defined in the Options section.

Group Mappings

Group mappings file can be used to group columns and sum values they contains. You can load such a file via the Import Mapping tool button.

Group mapping files are simple text files that should follow the following scheme:

GROUP_group1=filename1.mzXML
GROUP_group2=filename2.mzXML;filename3.mzXML

The example below can be translated as

Create a group named group1 containing columns filename1.mzXML and a group group1 containing columns filename2.mzXML and filename3.mzXML

If a column does not exists, it is simply ignored. Groups can be empty. Group columns are identified with the Import Mapping icon.