addGeneStatistics: addGeneStatistics

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

adds gene statistics to the giotto object

Usage

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

Arguments

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 gene metadata:

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

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

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

• mean_expr: Average gene expression in all cells

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

Value

giotto object if return_gobject = TRUE

Examples

data(mini_giotto_single_cell)

updated_giotto_object = addGeneStatistics(mini_giotto_single_cell)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.