Calculate Gene Signature Enrichment Score With Hypergeometric Test

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

A data.table with enrichment results.

Details

The enrichment score is calculated based on the p-value from the hypergeometric test:

\[-log10(p-value)\]