View source: R/spatial_enrichment.R
runPAGEEnrich_OLD | R Documentation |
Function to calculate gene signature enrichment scores per spatial position using PAGE.
runPAGEEnrich_OLD(
gobject,
sign_matrix,
expression_values = c("normalized", "scaled", "custom"),
reverse_log_scale = TRUE,
logbase = 2,
output_enrichment = c("original", "zscore"),
p_value = FALSE,
n_times = 1000,
name = NULL,
return_gobject = TRUE
)
gobject |
Giotto object |
sign_matrix |
Matrix of signature genes for each cell type / process |
expression_values |
expression values to use |
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) |
n_times |
number of permutations to calculate for p_value |
name |
to give to spatial enrichment results, default = PAGE |
return_gobject |
return giotto object |
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.
data.table with enrichment results
makeSignMatrixPAGE
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.