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#

`gobject`	Giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`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

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.

Value#

data.table with enrichment results