addFeatStatistics#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_giotto.R#L2805

Description#

Adds feature statistics to the giotto object

Usage#

addFeatStatistics(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  detection_threshold = 0,
  return_gobject = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

feat_type

feature type

spat_unit

spatial unit

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 feature metadata:

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

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

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

  • mean_expr: Average feature expression in all cells

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

Value#

giotto object if return_gobject = TRUE