runSpatialEnrich.rst

runSpatialEnrich

runSpatialEnrich

Description

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

Usage

runSpatialEnrich(
  gobject,
  enrich_method = c("PAGE", "rank", "hypergeometric"),
  sign_matrix,
  expression_values = c("normalized", "scaled", "custom"),
  min_overlap_genes = 5,
  reverse_log_scale = TRUE,
  logbase = 2,
  p_value = FALSE,
  n_times = 1000,
  rbp_p = 0.99,
  num_agg = 100,
  max_block = 2e+07,
  top_percentage = 5,
  output_enrichment = c("original", "zscore"),
  name = NULL,
  verbose = TRUE,
  return_gobject = TRUE
)

Arguments

Argument	Description
gobject	Giotto object
enrich_method	method for gene signature enrichment calculation
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 (PAGE)
reverse_log_scale	reverse expression values from log scale
logbase	log base to use if reverse_log_scale = TRUE
p_value	calculate p-value (default = FALSE)
n_times	(page/rank) number of permutation iterations to calculate p-value
rbp_p	(rank) fractional binarization threshold (default = 0.99)
num_agg	(rank) number of top genes to aggregate (default = 100)
max_block	number of lines to process together (default = 20e6)
top_percentage	(hyper) percentage of cells that will be considered to have gene expression with matrix binarization
output_enrichment	how to return enrichment output
name	to give to spatial enrichment results, default = PAGE
verbose	be verbose
return_gobject	return giotto object

Details

For details see the individual functions:

• PAGE: list(list("runPAGEEnrich"))
• Rank: list(list("runRankEnrich"))
• Hypergeometric: list(list("runHyperGeometricEnrich"))

Value

Giotto object or enrichment results if return_gobject = FALSE