hyperGeometricEnrich

Source: R/spatial_enrichment.R

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