SpaCCI_region {SpaCCI}R Documentation

Infer Cell-Cell Interactions in a Specified Region

Description

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.

Usage

SpaCCI_region(
  gene_spot_df,
  spot_cell_prop_df,
  region_spot_IDs,
  matching_L_R_pairs,
  matching_L_R_pairs_info
)

Arguments

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 ligand_vector and receptor_vector.

matching_L_R_pairs_info

A data frame providing additional information for each ligand-receptor pair, such as pathway information.

Value

A list containing:

pvalue_df

A data frame of inferred interactions within the specified region, including information on ligand and receptor cell types, P-values, and adjusted P-values.


[Package SpaCCI version 1.0.2 Index]