rankEnrich¶
rankEnrich
Description¶
Function to calculate gene signature enrichment scores per spatial position using a rank based approach.
Usage¶
rankEnrich(...)
Arguments¶
Argument |
Description |
|---|---|
|
Arguments passed on to ``runRankEnrich` <#runrankenrich>`_ list(“n”, ” “, list(list(list(“gobject”)), list(“Giotto object”)), “n”, ” “, list(list(list(“sign_matrix”)), list(“Matrix of signature genes for each cell type / process”)), “n”, ” “, list(list(list(“expression_values”)), list(“expression values to use”)), “n”, ” “, list(list(list(“reverse_log_scale”)), list(“reverse expression values from log scale”)), “n”, ” “, list(list(list(“logbase”)), list(“log base to use if reverse_log_scale = TRUE”)), “n”, ” “, list(list(list(“output_enrichment”)), |
list("how to return enrichment output")), "\n", " ", list(list(list("ties_method")), list("how to handle rank ties")), "\n", " ", list(list(list("p_value")), list("calculate p-values (boolean, default = FALSE)")), "\n", " ", list(list(list("n_times")), list("number of permutations to calculate for p_value")), "\n", " ", list(list(list("rbp_p")), list("fractional binarization threshold (default = 0.99)")), "\n", " ", list(list(list("num_agg")), list("number of top genes to aggregate (default = 100)")),
"\n", " ", list(list(list("name")), list("to give to spatial enrichment results, default = rank")), "\n", " ", list(list(list("return_gobject")), list("return giotto object")), "\n", " ")
Seealso¶
``runRankEnrich` <#runrankenrich>`_