findInteractionChangedFeats

findInteractionChangedFeats

Description

Identifies cell-to-cell Interaction Changed Features (ICF),

i.e. features that are differentially expressed due to proximity to other cell types.#’

Usage

findInteractionChangedFeats(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = "normalized",
  selected_feats = 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,
  set_seed = TRUE,
  seed_number = 1234
)

Arguments

Argument	Description
gobject	giotto object
feat_type	feature type
spat_unit	spatial unit
expression_values	expression values to use
selected_feats	subset of selected features (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
set_seed	set a seed for reproducibility
seed_number	seed number

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:

• features: All or selected list of tested features

• sel: average feature expression in the interacting cells from the target cell type

• other: average feature 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

Value

cpgObject that contains the Interaction Changed differential gene scores