addFeatStatistics: Add feature statistics

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

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

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.