identifyEnrichedInteractions: Identify all the significant interactions (L-R pairs) from...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Identify all the significant interactions (L-R pairs) from some cell groups to other cell groups

Description

Identify all the significant interactions (L-R pairs) from some cell groups to other cell groups

Usage

identifyEnrichedInteractions(
  object,
  from,
  to,
  bidirection = FALSE,
  pair.only = TRUE,
  pairLR.use0 = NULL,
  thresh = 0.05
)

Arguments

object	CellChat object
from	a vector giving the index or the name of source cell groups
to	a corresponding vector giving the index or the name of target cell groups. Note: The length of 'from' and 'to' must be the same, giving the corresponding pair of cell groups for communication.
bidirection	whether show the bidirectional communication, i.e., both 'from'->'to' and 'to'->'from'.
pair.only	whether only return ligand-receptor pairs without pathway names and communication strength
pairLR.use0	ligand-receptor pairs to use; default is all the significant interactions
thresh	threshold of the p-value for determining significant interaction

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.