Identify Cell-Cell Interaction Changed Genes (ICGs)

findCellProximityGenes()

Identifies cell-to-cell Interaction Changed Genes (ICG), i.e. genes that are differentially expressed due to proximity to other cell types.

findCellProximityGenes(...)

Arguments

…	Arguments passed on to findInteractionChangedGenes()
gobject	giotto object
expression_values	expression values to use
selected_genes	subset of selected genes (optional)
cluster_column	name of column to use for cell types
spatial_network_name	name of spatial network to use
minimum_unique_cells	minimum number of target cells required
minimum_unique_int_cells	minimum number of interacting cells required
diff_test	which differential expression test
mean_method	method to use to calculate the mean
offset	offset value to use when calculating log2 ratio
adjust_method	which method to adjust p-values
nr_permutations	number of permutations if diff_test = permutation
exclude_selected_cells_from_test	exclude interacting cells other cells
do_parallel	run calculations in parallel with mclapply
cores	number of cores to use if do_parallel = TRUE
set_seed	set a seed for reproducibility
seed_number	seed number

See also

findInteractionChangedGenes().