`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