filterGiotto

filter Giotto object based on expression threshold

filterGiotto(
  gobject,
  expression_values = c("raw", "normalized", "scaled", "custom"),
  expression_threshold = 1,
  gene_det_in_min_cells = 100,
  min_det_genes_per_cell = 100,
  verbose = F
)

Arguments

gobject

giotto object

expression_values

expression values to use

expression_threshold

threshold to consider a gene expressed

gene_det_in_min_cells

minimum # of cells that need to express a gene

min_det_genes_per_cell

minimum # of genes that need to be detected in a cell

verbose

verbose

Value

giotto object

Details

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

Examples

data(mini_giotto_single_cell)
#> Warning: data set ‘mini_giotto_single_cell’ not found

filtered_gobject = filterGiotto(mini_giotto_single_cell,
                                gene_det_in_min_cells = 10,
                                min_det_genes_per_cell = 10)
#> Error in filterGiotto(mini_giotto_single_cell, gene_det_in_min_cells = 10,     min_det_genes_per_cell = 10): unused arguments (gene_det_in_min_cells = 10, min_det_genes_per_cell = 10)