hyperGeometricEnrich¶
hyperGeometricEnrich
Description¶
Function to calculate gene signature enrichment scores per spatial position using a hypergeometric test.
Usage¶
hyperGeometricEnrich(...)
Arguments¶
Argument |
Description |
|---|---|
|
Arguments passed on to ``runHyperGeometricEnrich` <#runhypergeometricenrich>`_ 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(“top_percentage”)), |
list("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("p_value")), list("calculate p-values (boolean, default = FALSE)")), "\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¶
``runHyperGeometricEnrich` <#runhypergeometricenrich>`_