- Go to the Cytoscape menu and select: Plugins → Random Network Plugin → Compare to Random Network
If the Compare Random Network sub menu is grayed out, make sure that there is a network open Cytoscape to compare.
- The following window will open:
There are two options: Compare the currently selected network to a randomized versions of itself.
Or to compare the network against random networks created by one of the random network models.
- Selecting the first option will open the window below:
For information on how to setup this stage, see the Randomization Tutorial. Notice that the number of networks to create field is no longer here, this option is substituted in the next pane. Fill out the form as you prefer and then click "Next" - The below panel allows users to create a number of randomized networks and analyze them according to a chosen set of metrics. When the results are compared to the metric results on an existing network, it should give an indication if the existing network in question has non-random properties (i.e. meaningful properties).
Metrics: These four check boxes represent the four different metrics offered by our plugin.
Threads to run: The number of threads to use while analyzing. This is automatically set to the number of available processors. Setting this value higher than the number of processors will not speed up the calculation. Setting this number lower will increase the amount of time required, but will free up other processors. This value must be an integer greater than 0.
Rounds to run: The number of rounds to run. This s
- Wait for the task to complete
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