runPAGEEnrich#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_enrichment.R#L729

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#

Argument

Description

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. list()

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

Seealso#

`makeSignMatrixPAGE <#makesignmatrixpage>`__