addGeneStatistics

Source: R/auxiliary_giotto.R

adds gene statistics to the giotto object

addGeneStatistics(
  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 gene metadata:

  • nr_cells: Denotes in how many cells the gene is detected

  • per_cells: Denotes in what percentage of cells the gene is detected

  • total_expr: Shows the total sum of gene expression in all cells

  • mean_expr: Average gene expression in all cells

  • mean_expr_det: Average gene expression in cells with detectable levels of the gene

Examples


data(mini_giotto_single_cell)

updated_giotto_object = addGeneStatistics(mini_giotto_single_cell)

#> 
#>  gene statistics has already been applied once, will be overwritten