PAGEEnrich¶
PAGEEnrich
Description¶
Function to calculate gene signature enrichment scores per spatial position using PAGE.
Usage¶
PAGEEnrich(...)
Arguments¶
Argument |
Description |
|---|---|
|
Arguments passed on to ``runPAGEEnrich` <#runpageenrich>`_ 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(“min_overlap_genes”)), list(“minimum number of overlapping genes in sign_matrix required to calculate enrichment”)), “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("p_value")), list("calculate p-values (boolean, default = FALSE)")), "\n", " ", list(list(list("include_depletion")), list("calculate both enrichment and depletion")), "\n", " ", list(list(list("n_times")), list("number of permutations to calculate for p_value")), "\n", " ",
list(list(list("max_block")), list("number of lines to process together (default = 20e6)")), "\n", " ", list(list(list("name")), list("to give to spatial enrichment results, default = PAGE")), "\n", " ", list(list(list("verbose")), list("be verbose")), "\n", " ", list(list(list("return_gobject")), list("return giotto object")), "\n", " ")
Seealso¶
``runPAGEEnrich` <#runpageenrich>`_