processGiotto

Source: R/auxiliary_giotto.R

Wrapper for the different Giotto object processing functions

processGiotto(
  gobject,
  filter_params = list(),
  norm_params = list(),
  stat_params = list(),
  adjust_params = list(),
  verbose = TRUE
)

Arguments

gobject

giotto object

filter_params

additional parameters to filterGiotto

norm_params

additional parameters to normalizeGiotto

stat_params

additional parameters to addStatistics

adjust_params

additional parameters to adjustGiottoMatrix

verbose

be verbose (default is TRUE)

Value

giotto object

Details

See filterGiotto, normalizeGiotto, addStatistics and adjustGiottoMatrix for more information about the different parameters in each step. If you do not provide them it will use the default values.

Examples


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

processed_object = processGiotto(mini_giotto_single_cell,
                                 filter_params = list(gene_det_in_min_cells = 10,
                                 min_det_genes_per_cell = 10))
#> 1. start filter step
#> Error: object 'mini_giotto_single_cell' not found