runHyperGeometricEnrich

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

runHyperGeometricEnrich(
  gobject,
  sign_matrix,
  expression_values = c("normalized", "scaled", "custom"),
  reverse_log_scale = TRUE,
  logbase = 2,
  top_percentage = 5,
  output_enrichment = c("original", "zscore"),
  p_value = FALSE,
  name = NULL,
  return_gobject = TRUE
)

Arguments

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

Value

data.table with enrichment results

Details

The enrichment score is calculated based on the p-value from the hypergeometric test, -log10(p-value).