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