Function to calculate gene signature enrichment scores per spatial position using PAGE.
runPAGEEnrich( gobject, sign_matrix, expression_values = c("normalized", "scaled", "custom"), min_overlap_genes = 5, reverse_log_scale = TRUE, logbase = 2, output_enrichment = c("original", "zscore"), p_value = FALSE, include_depletion = FALSE, n_times = 1000, max_block = 2e+07, name = NULL, verbose = TRUE, return_gobject = TRUE )
| gobject | Giotto object |
|---|---|
| sign_matrix | Matrix of signature genes for each cell type / process |
| expression_values | expression values to use |
| min_overlap_genes | minimum number of overlapping genes in sign_matrix required to calculate enrichment |
| reverse_log_scale | reverse expression values from log scale |
| logbase | log base to use if reverse_log_scale = TRUE |
| output_enrichment | how to return enrichment output |
| p_value | calculate p-values (boolean, default = FALSE) |
| include_depletion | calculate both enrichment and depletion |
| n_times | number of permutations to calculate for p_value |
| max_block | number of lines to process together (default = 20e6) |
| name | to give to spatial enrichment results, default = PAGE |
| verbose | be verbose |
| return_gobject | return giotto object |
data.table with enrichment results
sign_matrix: a binary matrix with genes as row names and cell-types as column names.
Alternatively a list of signature genes can be provided to makeSignMatrixPAGE, which will create
the matrix for you.
The enrichment Z score is calculated by using method (PAGE) from Kim SY et al., BMC bioinformatics, 2005 as \(Z = ((Sm – mu)*m^(1/2)) / delta\). For each gene in each spot, mu is the fold change values versus the mean expression and delta is the standard deviation. Sm is the mean fold change value of a specific marker gene set and m is the size of a given marker gene set.