addCellStatistics

addCellStatistics

Description

adds cells statistics to the giotto object

Usage

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

Arguments

Argument

Description

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)

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

Value

giotto object if return_gobject = TRUE

Examples

data(mini_giotto_single_cell)

updated_giotto_object = addCellStatistics(mini_giotto_single_cell)