PAGEEnrich

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

PAGEEnrich(...)

Arguments

...

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

Value

gene enrichment

See also

runPAGEEnrich