Entering edit mode
tjal0001
•
0
@tjal0001-20059
Last seen 5.1 years ago
Hi, I am using rsbml package in R to create a biological network in R. The problem is that it seems rsbml extracted wrong edges:
I created a graph using the following code:
g <- rsbml_graph(doc)
But I see edges are wrong. In cell designer, I have an edge from species 's2428' to 's2421'. But in the outcome of the following code, I have just 're629' and 're623'.
for (i in seq(1, length(distinctEdgeNum),by = 1)){
z=distinctEdgeNum[[i]]
if (from(z)=='s2428'){
print(z)}
else if (to(z)=='s2428'){
print(z)}}
First of all, I searched the Cell designer model and there is no 're629' and 're623' in the model. Second, why the correct edges are not extracted! I HIGHLYYY appreciate if someone could help me with this critical issue. distinctEdgeNum is generated using following code:
distinctEdgeNum=buildEdgeList(g)
Kind Regards,
Please provide a reproducible example, i.e., an example SBML file that demonstrates the problem.
Hi Michael,
Thanks for always helping me. I am working with mTOR signalling pathway and following are the codes: I added first two lines in case you need to install rsbml.
If you check the graph, you can see multiple edges specially between species started with 's' are not included in the graph!
Kind Regards,
Where can I get that file?
Sorry for delay Michael. Please find the file in the following link:
https://drive.google.com/open?id=11MM169V7H1wbt-51YfUbG0I5EnPh1f7G
I appreciate if someone could help me to understand the logic. I've read the documentation as well but have no idea why edges that I'm after are not retrieved?!
Kind Regards,