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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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generate_prioritization_tables is not working #206

Closed jcorder316 closed 11 months ago

jcorder316 commented 12 months ago

Hi Guys,

I followed the Vignette how how to perform the analysis of nichenetr and I got a problem in the step of generate_prioritization_tables

prior_table <- nichenetr::generate_prioritization_tables(processed_expr_table, processed_DE_table, ligand_activities, processed_condition_markers, prioritizing_weights)

I get this error:

Joining with by = join_by(sender, receiver, ligand, receptor)Joining with by = join_by(sender, ligand, lfc_ligand, p_val_ligand)Joining with by = join_by(ligand)Joining with by = join_by(receiver, receptor, lfc_receptor, p_val_receptor)Joining with by = join_by(sender, ligand, avg_ligand)Joining with by = join_by(receiver, receptor, avg_receptor)

do you have any Idea where the problem could be?

any help is highly appreciated

csangara commented 11 months ago

Hi,

That's a message that is printed by the dplyr::join function to indicate which columns are being used to merge (you can use suppressMessages around the code to silence this). If the resulting prior_table dataframe isn't empty, I would not worry about this.