combineICF: combineICF

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

combineICF

Description

Combine ICF scores in a pairwise manner.

Usage

combineICF(
  icfObject,
  selected_ints = NULL,
  selected_feats = NULL,
  specific_feats_1 = NULL,
  specific_feats_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,
  verbose = T
)

Arguments

icfObject	ICF (interaction changed feat) score object
selected_ints	subset of selected cell-cell interactions (optional)
selected_feats	subset of selected Feats (optional)
specific_feats_1	specific Featset combo (need to position match specific_genes_2)
specific_feats_2	specific Featset 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
verbose	verbose

Value

icfObject that contains the filtered differential feats scores

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.