extractEnrichedLR: Identify all the significant interactions (L-R pairs) and...

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) 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

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