rankEnrich

Function to calculate gene signature enrichment scores per spatial position using a rank based approach.

rankEnrich(...)

Arguments

...

...	Arguments passed on to `runRankEnrich` `gobject` Giotto object `sign_matrix` Matrix of signature genes for each cell type / process `expression_values` expression values to use `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 `ties_method` how to handle rank ties `p_value` calculate p-values (boolean, default = FALSE) `n_times` number of permutations to calculate for p_value `rbp_p` fractional binarization threshold (default = 0.99) `num_agg` number of top genes to aggregate (default = 100) `name` to give to spatial enrichment results, default = rank `return_gobject` return giotto object

Arguments passed on to runRankEnrich