Identify Cell-Cell Interaction Changed Genes (ICGs)¶

findInteractionChangedGenes()

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

findInteractionChangedGenes(
    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 = 1000,
    exclude_selected_cells_from_test = T,
    do_parallel = TRUE,
    cores = NA,
    set_seed = TRUE,
    seed_number = 1234
)

Arguments¶

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

Value¶

A cpgObject that contains the Interaction Changed Genes’ differential 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
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
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