Calculate Spot Level Enrichment Scores for Pathways Using CAESAR

Source: R/caesar_enrichscore.R

This function calculates spot level enrichment scores for a list of pathways based on a cell-gene distance matrix in a Seurat object. The function uses a permutation-based approach to determine the significance of the enrichment scores.

CAESAR.enrich.score(
  seu,
  pathwaylist,
  assay.dist = "distce",
  reduction.name = "caesar",
  gene.use = NULL,
  n_fake = 1001,
  seed = 1
)

Arguments

seu

A Seurat object containing the gene expression data.

pathwaylist

A list of pathways, where each pathway is represented by a vector of genes.

assay.dist

A character string specifying the assay that contains the distance matrix. Default is "distce".

reduction.name

A character string specifying the reduction method to use if the distance matrix needs to be computed. Default is "caesar".

gene.use

A character vector specifying which genes to use in the analysis. If NULL, all genes in the distance matrix will be used. Default is NULL.

n_fake

An integer specifying the number of random permutations to generate for significance testing. Default is 1001.

seed

An integer specifying the random seed for reproducibility. Default is 1.

Value

A matrix of enrichment scores with cells as rows and pathways as columns.

Examples

data(toydata)

seu <- toydata$seu
pathway_list <- toydata$pathway_list

enrich.score <- CAESAR.enrich.score(seu, pathway_list)
#> Calculate co-embedding distance...
#> There are 2 pathways. The largest pathway has 48 genes.
#> Pathways with 37 genes finished, which includes 1 pathways, elapsed time is 1s.
#> Pathways with 48 genes finished, which includes 1 pathways, elapsed time is 0.05s.
head(enrich.score)
#>       GOBP_VASCULATURE_DEVELOPMENT GOBP_T_CELL_ACTIVATION
#> 24387                    0.8761239            0.000000000
#> 4049                     0.3816184            0.001998002
#> 11570                    0.2707293            0.001998002
#> 25172                    0.2807193            0.000999001
#> 32617                    0.9280719            0.997002997
#> 13902                    0.3096903            0.000000000