datasome
commented
4 months ago Hi Pedramto89,
The location information (see cols: peripheral, transmembrane, secreted, receptor and integrin in https://github.com/ventolab/cellphonedb-data/blob/master/data/protein_input.csv) is a characteristic of the protein and we could assume that this is where the interaction would happen, but we do not have a validated evidence). The above caveat not withstanding, in short you can filter the interactions if they involve at least one protein that is a receptor, transmembrane, or integrin, etc
Hope that helps,
Robert.
Hi.
I did the protein-protein interactions (PPIs) analysis and I have the csv file now after I melted the results. Now, I am wondering how can I filter the PPIs based on their location, limited to surface proteins? Thanks!
This is the summary of my data:
`> summary(cpdb) id_cp_interaction interacting_pair partner_a partner_b gene_a gene_b
Length:47088 Length:47088 Length:47088 Length:47088 Length:47088 Length:47088
Class :character Class :character Class :character Class :character Class :character Class :character
Mode :character Mode :character Mode :character Mode :character Mode :character Mode :character
secreted receptor_a receptor_b annotation_strategy is_integrin Interacting_cell
Length:47088 Length:47088 Length:47088 Length:47088 Length:47088 Length:47088
Class :character Class :character Class :character Class :character Class :character Class :character
Mode :character Mode :character Mode :character Mode :character Mode :character Mode :character
Relevance Cell_a Cell_b Mean Zscore Mean_scaled
Min. : 0.11 Length:47088 Length:47088 Min. : 0.0000 Min. :-0.3119 Min. :-2.2181
1st Qu.: 0.28 Class :character Class :character 1st Qu.: 0.0660 1st Qu.:-0.2845 1st Qu.:-0.7732
Median : 0.51 Mode :character Mode :character Median : 0.1470 Median :-0.2508 Median :-0.2126
Mean : 1.91 Mean : 0.7497 Mean : 0.0000 Mean : 0.0000
3rd Qu.: 1.27 3rd Qu.: 0.3500 3rd Qu.:-0.1663 3rd Qu.: 0.6463
Max. :19.17 Max. :31.8040 Max. :12.9219 Max. : 4.0551
NA's :41778`