findICG

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

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

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

• 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