Add Gene Statistics

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