rankEnrich: rankEnrich

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

rankEnrich

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 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

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.