The scDiffCom Class

An object of this class stores the intercellular communication results obtained when calling run_interaction_analysis.

Slots

parameters

List of parameters passed to run_interaction_analysis and used to build the object.

cci_table_raw

Data.table with all hypothetic CCIs induced from the original Seurat object and the internal LRI database. Can be erased with EraseRawCCI to obtain a lighter object, but might be worth keeping if one intends to modify the filtering parameters (see also our vignette).

cci_table_detected

Data.table with only the detected CCIs. If cci_table_raw is not NULL, can be updated with new filtering parameters without running the full permutation analysis (see FilterCCI).

ora_table

List of data.tables with the results of the over-representation analysis for each category. Results for additional categories can be added with RunORA.

distributions

List of matrices with the null distributions of each CCI. NULL by default.