possible_L_R_pairs_Cellinker {SpaCCI} | R Documentation |
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.
possible_L_R_pairs_Cellinker(
species,
gene_spot_expression_dataframe,
percentage
)
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. |
A list containing:
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.
A data frame with detailed information about the identified L-R pairs, including their original annotations from the Cellinker dataset.