hyperGeometricEnrich#

Last Updated: Mar 11, 2023

Description#

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

hyperGeometricEnrich(...)

...

Arguments passed on to runHyperGeometricEnrich

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