scDiffCom-class: The scDiffCom Class

In scDiffCom: Differential Analysis of Intercellular Communication from scRNA-Seq Data

The scDiffCom Class

Description

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.

scDiffCom documentation built on Nov. 4, 2023, 1:06 a.m.