runSpatialEnrich: runSpatialEnrich

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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"),
  reverse_log_scale = TRUE,
  logbase = 2,
  p_value = FALSE,
  n_times = 1000,
  top_percentage = 5,
  output_enrichment = c("original", "zscore"),
  name = NULL,
  return_gobject = TRUE
)

Arguments

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
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
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
return_gobject	return giotto object

Details

For details see the individual functions:

• PAGE: runPAGEEnrich

• Rank: runRankEnrich

• Hypergeometric: runHyperGeometricEnrich

Value

Giotto object or enrichment results if return_gobject = FALSE

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.