possible_L_R_pairs_Cellinker {SpaCCI}R Documentation

Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication

Description

Cellinker Database: This function identifies possible ligand-receptor (L-R) pairs for cell-cell communication analysis using data from the Cellinker 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.

Usage

possible_L_R_pairs_Cellinker(
  species,
  gene_spot_expression_dataframe,
  percentage
)

Arguments

species

A string specifying the species ("Human" or "Mouse"). The function selects the appropriate Cellinker interaction file based on this input.

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.

Value

A list containing:

possible_L_R_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_L_R_pairs_details

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


[Package SpaCCI version 1.0.2 Index]