CellChat (version 1.0.0)

extractEnrichedLR: Identify all the significant interactions (L-R pairs) and related signaling genes for a given signaling pathway

Description

Identify all the significant interactions (L-R pairs) and related signaling genes for a given signaling pathway

Usage

extractEnrichedLR(
  object,
  signaling,
  geneLR.return = FALSE,
  enriched.only = TRUE,
  thresh = 0.05,
  geneInfo = NULL,
  complex_input = NULL
)

Arguments

object

CellChat object

signaling

a char vector containing signaling pathway names for searching

geneLR.return

whether return the related signaling genes of enriched L-R pairs

enriched.only

whether only return the identified enriched signaling genes in the database. Default = TRUE, returning the significantly enriched signaling interactions

thresh

threshold of the p-value for determining significant interaction

geneInfo

a dataframe with gene official symbol (there should be one column named `Symbol`)

complex_input

signaling complex information from CellChatDB

Value

The returned value depends on the input argument:

When `geneLR.return = FALSE`, it returns a data frame containing the significant interactions (L-R pairs)

When `geneLR.return = TRUE`, it returns a list, the first element is a data frame containing the significant interactions (L-R pairs), and the second is a vector containing the related signaling genes of enriched L-R pairs, which can be used for examining the gene expression pattern using the function plotGeneExpression