runPAGEEnrich
¶
runPAGEEnrich
Description¶
Function to calculate gene signature enrichment scores per spatial position using PAGE.
Usage¶
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¶
Argument 
Description 


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 pvalues (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¶
 sign_matrix: a binary matrix with genes as row names and celltypes as column names.
Alternatively a list of signature genes can be provided to makeSignMatrixPAGE, which will create the matrix for you. list()
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
Seealso¶
``makeSignMatrixPAGE` <#makesignmatrixpage>`_