Filter ICGs

filterInteractionChangedGenes()

Filter Interaction Changed Genes’ (ICGs) Scores .

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

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

A cpgObject that contains the Interaction Changed Genes’ differential scores.