rankEnrich

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Last Updated: Mar 11, 2023

Description

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

Usage

rankEnrich(...)

Arguments

...

Arguments passed on to runRankEnrich 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 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