filterICF: filterICF

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

filterICF

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

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

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