filterCellProximityGenes: filterCellProximityGenes

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Filter cell proximity gene scores.

Usage

filterCellProximityGenes(
  cpgObject,
  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", "genes"),
  direction = c("both", "up", "down")
)

Arguments

cpgObject	cell proximity gene 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 genes
direction	differential expression directions to keep

Value

cpgObject that contains the filtered differential gene scores

Examples

    filterCellProximityGenes(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.