runPAGEEnrich: runPAGEEnrich

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

runPAGEEnrich

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

See Also

makeSignMatrixPAGE

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.