combineICF#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction.R#L1930

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#

Argument

Description

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