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

See also

runRankEnrich