RRA interactions — rra_interactions • scrnaseq.cellcomm

Rank interactions based on CellChat, LIANA (use all methods), cell2cell and CellPhoneDB

Usage

rra_interactions(
  cellchat_obj,
  liana_obj,
  cell2cell_obj,
  cpdb_obj,
  sample_id = NULL,
  output_dir = ".",
  n_perm = 1000
)

cellchat_obj: path to file generated by 'format_cellchat()'
liana_obj: path to file generated by 'format_liana()'
cell2cell_obj: path to file generated by 'format_cell2cell()'
cpdb_obj: path to file generated by 'format_cpdb()'
sample_id: sample id to use for saving object
output_dir: output directory for saving output (default = '.')
n_perm: number of permutations to create pval_dummy variable for computing -log10(pval_dummy) * score, only applicable to CellChat, Cell2Cell and CellPhoneDB