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
)Giotto object
Matrix of signature genes for each cell type / process
expression values to use
minimum number of overlapping genes in sign_matrix required to calculate enrichment
reverse expression values from log scale
log base to use if reverse_log_scale = TRUE
how to return enrichment output
calculate p-values (boolean, default = FALSE)
calculate both enrichment and depletion
number of permutations to calculate for p_value
number of lines to process together (default = 20e6)
to give to spatial enrichment results, default = PAGE
be verbose
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.