CellChat (version 1.0.0)

computeCommunProbPathway: Compute the communication probability on signaling pathway level by summarizing all related ligands/receptors

Description

Compute the communication probability on signaling pathway level by summarizing all related ligands/receptors

Usage

computeCommunProbPathway(object, thresh = 0.05)

Arguments

object

CellChat object

thresh

threshold of the p-value for determining significant interaction

Value

A CellChat object with updated slot 'netP':

object@netP$prob is the communication probability array on signaling pathway level; USER can convert this array to a data frame using the function 'reshape2::melt()',

e.g., `df.netP <- reshape2::melt(object@netP$prob, value.name = "prob"); colnames(df.netP)[1:3] <- c("source","target","pathway_name")` or access all significant interactions using the function subsetCommunication

object@netP$pathways list all the signaling pathways with significant communications