Calculate Gene Signature Enrichment Score With RANK¶

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

rankEnrich()

Arguments¶

Note

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