findICGSpot: findICGSpot
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

findICGSpot

R Documentation

findICGSpot

Description

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

Usage

findICGSpot(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  ave_celltype_exp,
  selected_genes = NULL,
  spatial_network_name = "Delaunay_network",
  minimum_unique_cells = 5,
  minimum_unique_int_cells = 5,
  CCI_cell_score = 0.1,
  dwls_cutoff = 0.001,
  diff_test = "permutation",
  nr_permutations = 100,
  adjust_method = "fdr",
  do_parallel = TRUE,
  cores = 2,
  set_seed = TRUE,
  seed_number = 1234
)

Arguments

`gobject`	giotto object
`expression_values`	expression values to use
`ave_celltype_exp`	averege gene expression in each cell type
`selected_genes`	subset of selected genes (optional)
`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
`CCI_cell_score`	cell proximity score to filter no interacted cell
`dwls_cutoff`	cell type proportion cutoff to label the cell
`diff_test`	which differential expression test
`nr_permutations`	number of permutations if diff_test = permutation
`adjust_method`	which method to adjust p-values
`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

Details

Function to calculate if genes expreesion residual are differentially expressed in cell types when they interact (approximated by physical proximity) with other cell types. Gene expression residual calculated as: (observed expression in spot - cell_type_proportion * average_expressed_in_cell_type) 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 residual in the interacting cells from the target cell type
other: average gene expression residual in the NOT-interacting cells from the target cell type
pcc_sel: correlation between cell proximity score and expression residual in the interacting cells from the target cell type
pcc_other: correlation between cell proximity score and expression residual in the NOT-interacting cells from the target cell type
pcc_diff: correlation 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
unif_int: cell-cell interaction