addGeneStatistics — addGeneStatistics • Giotto

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

updated_giotto_object = addGeneStatistics(mini_giotto_single_cell)
#> Error in addGeneStatistics(mini_giotto_single_cell): could not find function "addGeneStatistics"