filterGiotto#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_giotto.R#L1765

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