identifyOverExpressedLigandReceptor: Identify over-expressed ligands and (complex) receptors...

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

Identify over-expressed ligands and (complex) receptors associated with each cell group

Description

This function identifies the over-expressed ligands and (complex) receptors based on the identified signaling genes from 'identifyOverExpressedGenes'.

Usage

identifyOverExpressedLigandReceptor(
  object,
  features.name = "features",
  features = NULL,
  return.object = TRUE
)

Arguments

object	CellChat object
features.name	a char name used for storing the over-expressed ligands and receptors in '[e-mail][[paste0(features.name, ".LR")]]'
features	a vector of features to use. default use all over-expressed genes in '[e-mail][[features.name]]'
return.object	whether returning a CellChat object. If FALSE, it will return a data frame containing over-expressed ligands and (complex) receptors associated with each cell group

Value

A CellChat object or a data frame. If returning a CellChat object, a new element named paste0(features.name, ".LR") will be added into the list '[e-mail]'

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