You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Sorry, me again. I am not sure whether this is a bug or just that no results were found with my dataset. When I run the following:
prioritized_tbl_oi_all = get_top_n_lr_pairs(multinichenet_output$prioritization_tables, 50, rank_per_group = FALSE)
I get an empty table:
However, there are plenty of data in multinichenet_output$prioritization_tables:
Even if I only ask for the top 1 result to be returned, the resulting table is empty. Can you please explain what the definition of top X results are? i.e. what is used to define a result making the top n list? Can you think why I may not have any results? I also tried changing rank_per_group = TRUE but that did not help. Any insight you could give would be appreciated. In case it is relevant, one of my groups has only 2 samples.
Thanks,
Catherine
The text was updated successfully, but these errors were encountered:
I have been trying to look into this further to understand why no results are returned when running get_top_n_lr_pairs. It seems that the reason for this is because in the table prioritization_tbl_oi all of the values in the fraction_expressing_ligand_receptor column are 0.
Similarly, in the same table, the columns for fraction_receptor_group and fraction_ligand_group also contain only 0s. Do you know why this might be?
get_top_n_lr_pairs filters LR pairs in such a way that they should be expressed in at least one sample in a certain group/condition. (definition of expressed: gene should be expressed in >=5% of cells of a cell type in a sample).
Since the underlying issue is here that no LR pairs are expressed (as mentioned in #23), I will close this one here since there is not issue in the get_top_n_lr_pairs function.
Hi,
Sorry, me again. I am not sure whether this is a bug or just that no results were found with my dataset. When I run the following:
prioritized_tbl_oi_all = get_top_n_lr_pairs(multinichenet_output$prioritization_tables, 50, rank_per_group = FALSE)
I get an empty table:
However, there are plenty of data in multinichenet_output$prioritization_tables:
Even if I only ask for the top 1 result to be returned, the resulting table is empty. Can you please explain what the definition of top X results are? i.e. what is used to define a result making the top n list? Can you think why I may not have any results? I also tried changing
rank_per_group = TRUE
but that did not help. Any insight you could give would be appreciated. In case it is relevant, one of my groups has only 2 samples.Thanks,
Catherine
The text was updated successfully, but these errors were encountered: