combineInteractionChangedGenes

Combine ICG scores in a pairwise manner.

combineInteractionChangedGenes(
  cpgObject,
  selected_ints = NULL,
  selected_genes = NULL,
  specific_genes_1 = NULL,
  specific_genes_2 = NULL,
  min_cells = 5,
  min_int_cells = 3,
  min_fdr = 0.05,
  min_spat_diff = 0,
  min_log2_fc = 0.5,
  do_parallel = TRUE,
  cores = NA,
  verbose = T
)

Arguments

cpgObject

ICG (interaction changed gene) score object

selected_ints

subset of selected cell-cell interactions (optional)

selected_genes

subset of selected genes (optional)

specific_genes_1

specific geneset combo (need to position match specific_genes_2)

specific_genes_2

specific geneset combo (need to position match specific_genes_1)

min_cells

minimum number of target cell type

min_int_cells

minimum number of interacting cell type

min_fdr

minimum adjusted p-value

min_spat_diff

minimum absolute spatial expression difference

min_log2_fc

minimum absolute log2 fold-change

do_parallel

run calculations in parallel with mclapply

cores

number of cores to use if do_parallel = TRUE

verbose

verbose

Value

cpgObject that contains the filtered differential gene scores