Anchor Extension:
When determining the nodes of the network, the anchor extension parameter extends span of the interaction anchors in order to add flexibility when grouping anchors into nodes where the interactions between the anchors will form the edges. The extension parameter is used only to merge locations. Regions for nodes are based on the minimum and maximum locations of the anchors defining the node.



Min PET:
To look only at strongly connected networks, the min PET parameter allows for filtering the edges such that only edges with at least this many PETs will be shown. The PET count for the network is defined as the sum of all the PETs from the interactions forming the edge in the network.
In the above example, since the min PET parameter is set to 6, the edge with only 5 for its PET count is removed.
Finally if a node is left without any edges, it is remove from the network.



Max Intra-Chromosome Distance/Min PET Exceeding Intra-Chromosome Distance:
For interactions occuring on the same chromosome, interactions with very long distances between them may be unlikely. To account for this, the max-intra-chromsome distance parameter allows for setting a maximum distance for edges to consider. For flexibility, the Min PET Exceeding Intra-Chromosome Distance parameter allows for keeping some of these long distant interactions if there is a high enough PET count.
Considering the above example, there are two long distant interactions defined as edges.
Only the edge with the PET above the threshold provided is kept in the network.



Min PET For Inter-chromosome Edges:
Although inter-chromsome occur, they can be unlikely occurrences. To take these interactions into account the min PET for inter-chromosome edges parameter filters edges, leaving only inter-chromosome edges above the PET threshold.
In the above example, two inter-chromosome edges exist in the component.
Only the inter-chromsome edge with a high enough PET count remains as an edge in the network.



Minimum Component Size/Min PET Below Component Size:
The minimum component size parameter allows for filtering components such that only components with at least the specified number of nodes are provided. Setting this number to a high value allows for only considering highly connected networks. The Min PET below component size parameter adds flexibility in that it allows for keeping components that have an edge with a high PET count.
In the above example, the first component will be in the network because the number of nodes satisfies the min-size parameter.
The third component will also be in the network because although it doesn't have the sufficient number of nodes, it has an interaction with a high enough PET count.
This leaves the second component as not being in the network because it fails to satisfy either criteria