Calculate Position Gene Signature Enrichment With PAGE¶

runPAGEEnrich()

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
)

Arguments¶

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

Value¶

A data.table with enrichment results.

Details¶

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.