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

findICG(
gobject,
expression_values = "normalized",
selected_genes = NULL,
cluster_column,
spatial_network_name = "Delaunay_network",
minimum_unique_cells = 1,
minimum_unique_int_cells = 1,
diff_test = c("permutation", "limma", "t.test", "wilcox"),
mean_method = c("arithmic", "geometric"),
offset = 0.1,
adjust_method = c("bonferroni", "BH", "holm", "hochberg", "hommel", "BY", "fdr",
"none"),
nr_permutations = 100,
exclude_selected_cells_from_test = T,
do_parallel = TRUE,
cores = NA,
set_seed = TRUE,
seed_number = 1234
)

## Arguments

gobject giotto object expression values to use subset of selected genes (optional) name of column to use for cell types name of spatial network to use minimum number of target cells required minimum number of interacting cells required which differential expression test method to use to calculate the mean offset value to use when calculating log2 ratio which method to adjust p-values number of permutations if diff_test = permutation exclude interacting cells other cells run calculations in parallel with mclapply number of cores to use if do_parallel = TRUE set a seed for reproducibility seed number

## Value

cpgObject that contains the differential gene scores

## Details

Function to calculate if genes are differentially expressed in cell types when they interact (approximated by physical proximity) with other cell types. 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 in the interacting cells from the target cell type

• other: average gene expression in the NOT-interacting cells from the target cell type

• log2fc: log2 fold-change between sel and other

• diff: spatial expression difference between sel and other

• p.value: associated 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

• nr_other: number of other cells of selected target cell type

• int_nr_other: number of other cells for interacting cell type

• unif_int: cell-cell interaction