processGiotto: processGiotto

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

processGiotto

Description

Wrapper for the different Giotto object processing functions

Usage

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)

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.

Value

giotto object

Examples

data(mini_giotto_single_cell)

processed_object = processGiotto(mini_giotto_single_cell,
                                 filter_params = list(gene_det_in_min_cells = 10,
                                 min_det_genes_per_cell = 10))

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.