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 )
| 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 |
data.table with enrichment results
The enrichment score is calculated based on the p-value from the hypergeometric test, -log10(p-value).