Coexpression function

[elenadelpup]

Add a coexpression function that uses coexpression edges to merge functional clusters.

[kumarsaurabh20]

Hi @elenadelpup,

There are two conflicts as mentioned above. Please make sure you structure the arguments section as present in the current version and also make changes in the table_name as it is present in the current version. I can't see how I could resolve this conflict, but maybe you could do it from your side and then commit your changes.

[elenadelpup]

Hi Kumar, Ok, I will fix that from my side. Can you please share with me the latest version of the arguments that I should consider? So that I am sure I am looking at the right thing. I thought I fixed tablename • table_name everywhere but I will doublecheck. Best, Elena From: Kumar Saurabh Singh ***@***.***> Date: Monday, 20 January 2025 at 14:40 To: kumarsaurabh20/meantools ***@***.***> Cc: Elena Del Pup ***@***.***>, Mention ***@***.***> Subject: Re: [kumarsaurabh20/meantools] Coexpression function (PR #1) Hi @elenadelpup<https://github.com/elenadelpup>, There are two conflicts as mentioned above. Please make sure you structure the arguments section as present in the current version and also make changes in the table_name as it is present in the current version. I can't see how I could resolve this conflict, but maybe you could do it from your side and then commit your changes. — Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO4VVF6UBZIOBLISHJSOKUD2LT4F3AVCNFSM6AAAAABT7CYUMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMBSGQ2TMNZUHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[kumarsaurabh20]

The current structure is on the main branch.
https://github.com/kumarsaurabh20/meantools/blob/main/merge_clusters.py

Once there are no conflicts I merge the branches?

[kumarsaurabh20]

@elenadelpup For the table name use the following:

tablename = "Combine_MC"

if Options.decay_rate:
table_name = tablename + "DR" + str(Options.decay_rate)
gizmos.export_to_sql(Options.sqlite_db_name, merged_df, table_name, index=False)

[kumarsaurabh20]

@elenadelpup Also with the test data, I expected to get multiple rows based on the coexpression data. But What I see is just one row with all the metabolites and genes combined. It is a bit weird. I am not sure why we are getting this kind of results. I will test it at my end once again and let you know. At this moment, in the coexpression table, there are weak links and very strong links. The script considers one coexpression network at a time. So perhaps the script considers everything (all weak and strong links combined) and merges everything in one merge table.