Calculate Gene Signature Enrichment With PAGE¶

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

PAGEEnrich()

Arguments¶

Note

Arguments passed on to runPAGEEnrich()

gobject	Giotto object
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