LR_database {SpaCCI} | R Documentation |
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 = 10
)
Arguments
species |
A string specifying the species ( |
database_name |
A string specifying the L-R database to use. Options include |
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 |
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.
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)