filterInteractionChangedGenes

filterInteractionChangedGenes

Description

Filter Interaction Changed Gene scores.

Usage

filterInteractionChangedGenes(
  cpgObject,
  min_cells = 4,
  min_cells_expr = 1,
  min_int_cells = 4,
  min_int_cells_expr = 1,
  min_fdr = 0.1,
  min_spat_diff = 0.2,
  min_log2_fc = 0.2,
  min_zscore = 2,
  zscores_column = c("cell_type", "genes"),
  direction = c("both", "up", "down")
)

Arguments

Argument

Description

cpgObject

ICG (interaction changed gene) score object

min_cells

minimum number of source cell type

min_cells_expr

minimum expression level for source cell type

min_int_cells

minimum number of interacting neighbor cell type

min_int_cells_expr

minimum expression level for interacting neighbor cell type

min_fdr

minimum adjusted p-value

min_spat_diff

minimum absolute spatial expression difference

min_log2_fc

minimum log2 fold-change

min_zscore

minimum z-score change

zscores_column

calculate z-scores over cell types or genes

direction

differential expression directions to keep

Value

cpgObject that contains the filtered differential gene scores