Combine ICG Scores (Pairwise)

combineICG()

Combine ICG scores in a pairwise manner.

combineICG(
    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

A cpgObject that contains the filtered differential gene scores.