filterICG — filterICG • Giotto

Filter Interaction Changed Gene scores.

filterICG(
  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

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