filterICF#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction.R#L1425

Description#

Filter Interaction Changed Feature scores.

Usage#

filterICF(
  icfObject,
  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", "feats"),
  direction = c("both", "up", "down")
)

Arguments#

Argument

Description

icfObject

ICF (interaction changed feature) 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 features

direction

differential expression directions to keep

Value#

icfObject that contains the filtered differential feature scores