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addFeatStatistics.md

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addFeatStatistics

Add feature statistics

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