GraphML output has unconnected nodes

[imaigene]

Hello,

I am checking the output of intra_network that generated a graphml network and I find that a part of a big network that starts from my gene of interest there are 3 other smaller network that do not have any connecting edges to the main network. Is that expected? How should I interpret these nodes, in the sense of why do they come up as downstream if they are not in anyway connected to my gene of interest? Cheers,

Maria

[SCA-IRCM]

Hi,

The other smaller networks must be indirectly connected to your gene of interest. The function contains several steps to first simplify the network and then add information from the ligands associated with your receptors of interest. To avoid these sub-networks to appear you can set the connected parameter of the function to TRUE, then it will keep only the genes connected to the gene of interest.

Thanks for using SingleCellSignalR!

SCA