runHyperGeometricEnrich#

Last Updated: Mar 11, 2023

Description#

Function to calculate gene signature enrichment scores per spatial position using a hypergeometric test.

Usage#

runHyperGeometricEnrich(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  sign_matrix,
  expression_values = c("normalized", "scaled", "custom"),
  reverse_log_scale = TRUE,
  logbase = 2,
  top_percentage = 5,
  output_enrichment = c("original", "zscore"),
  p_value = FALSE,
  name = NULL,
  return_gobject = TRUE
)

Arguments#

`gobject`	Giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`sign_matrix`	Matrix of signature genes for each cell type / process
`expression_values`	expression values to use
`reverse_log_scale`	reverse expression values from log scale
`logbase`	log base to use if reverse_log_scale = TRUE
`top_percentage`	percentage of cells that will be considered to have gene expression with matrix binarization
`output_enrichment`	how to return enrichment output
`p_value`	calculate p-values (boolean, default = FALSE)
`name`	to give to spatial enrichment results, default = hypergeometric
`return_gobject`	return giotto object

Details#

The enrichment score is calculated based on the p-value from the hypergeometric test, -log10(p-value).

Value#

data.table with enrichment results