findCellProximityGenes_per_interaction: findCellProximityGenes_per_interaction

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

findCellProximityGenes_per_interaction

Description

Identifies genes that are differentially expressed due to proximity to other cell types.

Usage

findCellProximityGenes_per_interaction(
  expr_values,
  cell_metadata,
  annot_spatnetwork,
  sel_int,
  cluster_column = NULL,
  minimum_unique_cells = 1,
  minimum_unique_int_cells = 1,
  exclude_selected_cells_from_test = T,
  diff_test = c("permutation", "limma", "t.test", "wilcox"),
  mean_method = c("arithmic", "geometric"),
  offset = 0.1,
  adjust_method = "bonferroni",
  nr_permutations = 100,
  cores = 1,
  set_seed = TRUE,
  seed_number = 1234
)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.