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Subset calculation

The following dialog will appear only if you have set edges or vertices as your calculation target. It enables you to calculate either the Pairwise Disconnectivity Index (PDI) for all vertices/edges of your network or to upload a subset file and calculate the PDI for only those vertices or edges that are listed in the subset file:



If you don't want to calculate a subset (i.e., calculate all vertices/edges), leave the radio button (A) set to "No subset".

If you wish to upload and calculate a subset instead, set the radio button (A) to "Upload Subset" and click the Browse button at the file dialog (B).

Upload a subset of vertices


If you wish to calculate a subset of vertices the contents the file may contain single vertices as well as groups of vertices. A group of vertices is a collection of at least two vertices. Similar to a multiple gene knockout in the lab, the PDI for a group of vertices is calculated for the whole collection instead of each vertex separately.
Write the name of a vertex in the uploaded network file in a row in case of a single vertex, i.e.

[Vertex]

or specify a group of vertices by placing the names of several vertices in the uploaded network file in a row. In this case, you must use the same delimiter as the previously uploaded network file to distinguish between the vertices of a group (delimiter is shown at (C)), i.e.

[Vertex1] [separator] [Vertex2] [separator] [Vertex3] ...

Example: Recall the network
A;B
B;C
B;D
C;D
C;E
D;B

You wish to estimate the PDI for the vertices A and B. In addition, you're interested in the vertices A, B and C as a group of vertices. The corresponding subset file would be:
A
B
A;B;C

Upload a subset of edges


If you wish to calculate a subset of edges the contents the file may contain single edges as well as groups of edges. A group of edges is a collection of at least two edges. Similar to a multiple gene knockout in the lab, the PDI for a group of edges is calculated for the whole collection instead of each edges separately.
In case of a single edge, specify the edge in the same way as in the uploaded network file, i.e.

[fromVertex ] [separator] [toVertex]

or declare a group of edges by specifying several edges in one row. Each edge must be indicated in the same way as in the uploaded network file and you must use the same delimiter to distinguish between the edges of a group (delimiter is shown at (C)), i.e.

[fromVertex ] [separator] [toVertex] [separator] [fromVertex ] [separator] [toVertex] ...

Example: In the example network given above, you wish to estimate the PDI for the edges A;B and B;D. In adidtion, you're interested in them as a group of edges. The corresponding subset file would be:
A;B
B;D
A;B;B;D


Please note: If you selected one of our example networks, the upload subset functionality is deactivated and you'll have to use the preselected subset given by DiVa online for the corresponding example network.

If you have finished move on to the next dialog by hitting the "Next" button or go back one step by using the "Previous" button.


 
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...::: Department of Bioinformatics, Center of Informatics,Statistics and Epidemiology UMG, University of Göttingen :::...