addCellStatistics#

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Last Updated: Mar 11, 2023

Description#

adds cells statistics to the giotto object

Usage#

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

Arguments#

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 cell metadata:

  • nr_feats: Denotes in how many features are detected per cell

  • perc_feats: Denotes what percentage of features is detected per cell

  • total_expr: Shows the total sum of feature expression per cell

Value#

giotto object if return_gobject = TRUE