addCellStatistics

adds cells statistics to the giotto object

addCellStatistics(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  detection_threshold = 0,
  return_gobject = TRUE
)

Arguments

gobject

giotto object

expression_values

expression values to use

detection_threshold

detection threshold to consider a gene detected

return_gobject

boolean: return giotto object (default = TRUE)

Value

giotto object if return_gobject = TRUE

Details

This function will add the following statistics to cell metadata:

• nr_genes: Denotes in how many genes are detected per cell

• perc_genes: Denotes what percentage of genes is detected per cell

• total_expr: Shows the total sum of gene expression per cell

Examples

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

updated_giotto_object = addCellStatistics(mini_giotto_single_cell)
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found