CAESAR.Suite (version 0.1.0)

CAESAR.enrich.score: Calculate Spot Level Enrichment Scores for Pathways Using CAESAR

Description

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.

Usage

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

Value

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

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.

Examples

data(toydata)

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

enrich.score <- CAESAR.enrich.score(seu, pathway_list)
head(enrich.score)