PAGEEnrich#

Last Updated: May 20, 2025

Description#

Function to calculate gene signature enrichment scores per spatial position using PAGE.

PAGEEnrich(...)

...

Arguments passed on to runPAGEEnrich

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
min_overlap_genes: minimum number of overlapping genes in sign_matrix required to calculate enrichment
reverse_log_scale: reverse expression values from log scale
logbase: log base to use if reverse_log_scale = TRUE
output_enrichment: how to return enrichment output
p_value: calculate p-values (boolean, default = FALSE)
include_depletion: calculate both enrichment and depletion
n_times: number of permutations to calculate for p_value
max_block: number of lines to process together (default = 20e6)
name: to give to spatial enrichment results, default = PAGE
verbose: be verbose
return_gobject: return giotto object