filterICGSpot: filterICGSpot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

filterICGSpot

Description

Filter Interaction Changed Gene scores for spots.

Usage

filterICGSpot(
  cpgObject,
  min_cells = 4,
  min_cells_expr_resi = 0.05,
  min_int_cells = 4,
  min_int_cells_expr_resi = 0.05,
  min_fdr = 0.5,
  min_pcc_diff = 0.05,
  min_zscore = 0.05,
  zscores_column = c("cell_type", "genes"),
  direction = c("both", "up", "down")
)

Arguments

cpgObject	ICG (interaction changed gene) score object
min_cells	minimum number of source cell type
min_cells_expr_resi	minimum expression residual level for source cell type
min_int_cells	minimum number of interacting neighbor cell type
min_int_cells_expr_resi	minimum expression residual level for interacting neighbor cell type
min_fdr	minimum adjusted p-value
min_pcc_diff	minimum absolute pcc difference difference
min_zscore	minimum z-score change
zscores_column	calculate z-scores over cell types or genes
direction	differential expression directions to keep

Value

cpgObject that contains the filtered differential gene scores

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.