filterGiotto

filterGiotto

Description

filter Giotto object based on expression threshold

Usage

filterGiotto(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("raw", "normalized", "scaled", "custom"),
  expression_threshold = 1,
  feat_det_in_min_cells = 100,
  gene_det_in_min_cells = NULL,
  min_det_feats_per_cell = 100,
  min_det_genes_per_cell = NULL,
  poly_info = "cell",
  verbose = TRUE
)

Arguments

Argument	Description
gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
expression_values	expression values to use
expression_threshold	threshold to consider a gene expressed
feat_det_in_min_cells	minimum # of cells that need to express a feature
gene_det_in_min_cells	deprecated, use feat_det_in_min_cells
min_det_feats_per_cell	minimum # of features that need to be detected in a cell
min_det_genes_per_cell	deprecated, use min_det_feats_per_cell
poly_info	polygon information to use
verbose	verbose

Details

The function ``filterCombinations` <#filtercombinations>`_ can be used to explore the effect of different parameter values.

Value

giotto object