PAGEEnrich

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

PAGEEnrich(...)

Arguments

...

...	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

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