filterGiotto#

Last Updated: Jan 29, 2024

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,
  all_spat_units = TRUE,
  all_feat_types = TRUE,
  poly_info = "cell",
  tag_cells = FALSE,
  tag_cell_name = "tag",
  tag_feats = FALSE,
  tag_feats_name = "tag",
  verbose = TRUE
)

Arguments#

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

all_spat_units

apply features to remove filtering results from current spatial unit/feature type combination across ALL spatial units (default = TRUE)

all_feat_types

apply cells to remove filtering results from current spatial unit/feature type combination across ALL feature types (default = TRUE)

poly_info

polygon information to use

tag_cells

tag filtered cells in metadata vs. remove cells

tag_cell_name

column name for tagged cells in metadata

tag_feats

tag features in metadata vs. remove features

tag_feats_name

column name for tagged features in metadata

verbose

verbose

Details#

The function filterCombinations can be used to explore the effect of different parameter values.

Value#

giotto object