SpaCCI_region {SpaCCI} | R Documentation |
This function infers cell-cell interactions within a specified region using spatial transcriptomics data. It applies permutation testing to identify significant ligand-receptor interactions in the region.
SpaCCI_region(
gene_spot_df,
spot_cell_prop_df,
region_spot_IDs,
matching_L_R_pairs,
matching_L_R_pairs_info
)
gene_spot_df |
A data frame where the rows are genes and the columns are spots (Spot_IDs), representing gene expression levels across spatial spots. |
spot_cell_prop_df |
A data frame of cell type proportions for each spot. The rows represent spots (Spot_IDs), and the columns represent different cell types. |
region_spot_IDs |
A vector of Spot_IDs representing the spots included in the region of interest. |
matching_L_R_pairs |
A data frame containing matching ligand-receptor pairs. Each row corresponds to a ligand-receptor pair, with columns for |
matching_L_R_pairs_info |
A data frame providing additional information for each ligand-receptor pair, such as pathway information. |
A list containing:
A data frame of inferred interactions within the specified region, including information on ligand and receptor cell types, P-values, and adjusted P-values.