addGeneStatistics

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)