runPAGEEnrich#
Last Updated: Jan 14, 2025
Description#
Function to calculate gene signature enrichment scores per spatial position using PAGE.
Usage#
runPAGEEnrich(
gobject,
spat_unit = NULL,
feat_type = NULL,
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#
|
Giotto object |
|
spatial unit |
|
feature type |
|
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 |
Details#
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.
Value#
data.table with enrichment results
See Also#
makeSignMatrixPAGE