hyperGeometricEnrich

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

hyperGeometricEnrich(...)

Arguments

...

...	Arguments passed on to `runHyperGeometricEnrich` `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 `top_percentage` percentage of cells that will be considered to have gene expression with matrix binarization `output_enrichment` how to return enrichment output `p_value` calculate p-values (boolean, default = FALSE) `name` to give to spatial enrichment results, default = rank `return_gobject` return giotto object

Arguments passed on to runHyperGeometricEnrich

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
top_percentage: percentage of cells that will be considered to have gene expression with matrix binarization
output_enrichment: how to return enrichment output
p_value: calculate p-values (boolean, default = FALSE)
name: to give to spatial enrichment results, default = rank
return_gobject: return giotto object