Downstream pathways

[laetitiacollet]

Dear all,

I manage to implement the function but when I'm trying to find the downstream signaling the function ".checkReceptorSignaling" does not work. It tells me that the it does not find the Reactome / GOBP data. However, I don't know how to find this pathways in the right format with your package.

Could you please help me with this issue ?

With best regards,

[jcolinge]

Dear Laetitia,

What do you mean by "I managed to implement the function"? Which function?

.checkReceptorSignaling is a function that is private to the package (thus the dot at the beginning of its name). Were you trying to call it directly?

Best, Jacques

[laetitiacollet]

Dear Jacques,

thank for reply,

Yes i try to call the function directly pathways<-.checkReceptorSignaling(gene_matrix_prepare, results, reference="REACTOME") -gene_matrix_prepare is my gene matrix I transformed using the function prepareDataset -results is the dataframe i obtain with ligant / receptor and correlation for this matrix (with .getCorrelatedLR). But when i call the function .CheckReceptorSignaling I have an error message saying that "reactome" is not found. In the explanation on github you say that "Participation to a complex and being regulated as well as the pathway directed topologies are defined by Reactome and KEGG pathways as provided by PathwayCommons." Do I have to upload pathways form Pathwaycommons ?

Sorry for the question, I am just starting to using R.

Thank you in advance for your reply,

Laetitia

[jcolinge]

Again, because this function is private to the package, as the data frame reactome is, then it does not work from the outside.

There is no reason, especially as a beginner to call such functions that implement part of an analysis. You have to limit yourself to the function that provide the elementary analyses to the users. I strongly recommend that you take the example in BulkSignalR_companion/scripts/SDC-application.R and modify it to read and apply to your own data. Alternatively, if you work with spatial transcriptomics at medium resolution like Visium, then start from ST-application.R.

All the best, J