SpaCCI (version 1.0.4)

LR_database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication

Description

This function identifies possible ligand-receptor (L-R) pairs for cell-cell communication analysis using a selected database. It checks for the presence of all genes involved in each L-R pair within the provided gene expression matrix, filtering based on a specified expression percentage threshold. The function supports multiple databases including CellChat, CellPhoneDB, Cellinker, ICELLNET, and ConnectomeDB.

Usage

LR_database(
  species,
  database_name,
  gene_spot_expression_dataframe,
  percentage = NULL
)

Value

A list containing:

possible_LR_pairs

A data frame of L-R pairs where all genes are present in the gene_spot_expression_dataframe and meet the expression threshold. The data frame includes the ligand and receptor vectors, and the combined gene vectors.

possible_LR_pairs_info

A data frame with detailed information about the identified L-R pairs, including their original annotations from the selected database.

Arguments

species

A string specifying the species ("Human" or "Mouse").

database_name

A string specifying the L-R database to use. Options include "CellChat", "CellPhoneDB", "Cellinker", "ICELLNET", and "ConnectomeDB".

gene_spot_expression_dataframe

A gene expression data frame with genes as row names and Spot IDs as column names. This data frame is used to verify the presence of all genes involved in the L-R pairs.

percentage

A numeric value specifying the minimum percentage of spots in which a gene must be expressed to be considered. The default is 10, meaning the gene express over 10% of spots.

Examples

library(SpaCCI)
#Load the example data
data(test_data)
gene_spot_df <- test_data$gene_spot_df
result <- LR_database(species = "Human",
            database_name = "CellChat",
            gene_spot_expression_dataframe = gene_spot_df)