Identifies cell-to-cell Interaction Changed Genes (ICG) for spots, i.e. genes expression residual that are differentially due to proximity to other cell types.
findICGSpot(
gobject,
expression_values = c("normalized", "scaled", "custom"),
ave_celltype_exp,
selected_genes = NULL,
spatial_network_name = "Delaunay_network",
minimum_unique_cells = 5,
minimum_unique_int_cells = 5,
CCI_cell_score = 0.1,
dwls_cutoff = 0.001,
diff_test = "permutation",
nr_permutations = 100,
adjust_method = "fdr",
do_parallel = TRUE,
cores = 2,
set_seed = TRUE,
seed_number = 1234
)giotto object
expression values to use
averege gene expression in each cell type
subset of selected genes (optional)
name of spatial network to use
minimum number of target cells required
minimum number of interacting cells required
cell proximity score to filter no interacted cell
cell type proportion cutoff to label the cell
which differential expression test
number of permutations if diff_test = permutation
which method to adjust p-values
run calculations in parallel with mclapply
number of cores to use if do_parallel = TRUE
set a seed for reproducibility
seed number
cpgObject that contains the differential gene scores
Function to calculate if genes expreesion residual are differentially expressed in cell types when they interact (approximated by physical proximity) with other cell types. Gene expression residual calculated as: (observed expression in spot - cell_type_proportion * average_expressed_in_cell_type) The results data.table in the cpgObject contains - at least - the following columns:
genes: All or selected list of tested genes
sel: average gene expression residual in the interacting cells from the target cell type
other: average gene expression residual in the NOT-interacting cells from the target cell type
pcc_sel: correlation between cell proximity score and expression residual in the interacting cells from the target cell type
pcc_other: correlation between cell proximity score and expression residual in the NOT-interacting cells from the target cell type
pcc_diff: correlation difference between sel and other
p.value: associated p-value
p.adj: adjusted p-value
cell_type: target cell type
int_cell_type: interacting cell type
nr_select: number of cells for selected target cell type
int_nr_select: number of cells for interacting cell type
unif_int: cell-cell interaction