createSpatialEnrich

createSpatialEnrich

Description

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

Usage

createSpatialEnrich(...)

Arguments

Argument

Description

...

Arguments passed on to ``runSpatialEnrich` <#runspatialenrich>`_ list(“n”, ” “, list(list(list(“gobject”)), list(“Giotto object”)), “n”, ” “, list(list(list(“enrich_method”)), list(“method for gene signature enrichment calculation”)), “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("min_overlap_genes")), list("minimum number of overlapping genes in sign_matrix required to calculate enrichment (PAGE)")), "\n", "    ", list(list(list("logbase")), list("log base to use if reverse_log_scale = TRUE")), "\n", "    ", list(list(list("p_value")), list("calculate p-value (default = FALSE)")), "\n", "    ", list(list(list("n_times")), list("(page/rank) number of permutation iterations to calculate p-value")), "\n", "    ", list(list(list("rbp_p")), list("(rank) fractional binarization threshold (default = 0.99)")),
"\n", "    ", list(list(list("num_agg")), list("(rank) number of top genes to aggregate (default = 100)")), "\n", "    ", list(list(list("max_block")), list("number of lines to process together (default = 20e6)")), "\n", "    ", list(list(list("top_percentage")), list("(hyper) percentage of cells that will be considered to have gene expression with matrix binarization")), "\n", "    ", list(list(list("output_enrichment")), list("how to return enrichment output")), "\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

``runSpatialEnrich` <#runspatialenrich>`_