run_gsea: Run GSEA to compare a gene list(s) to per cell or per cluster...

In NCBI-Hackathons/RClusterCT: Classifier for Single-cell RNA-seq Using Cell Clusters

Run GSEA to compare a gene list(s) to per cell or per cluster expression data

Description

Use fgsea algorithm to compute normalized enrichment scores and pvalues for gene set ovelap

Usage

run_gsea(
  expr_mat,
  query_genes,
  cluster_ids = NULL,
  n_perm = 1000,
  per_cell = FALSE,
  scale = FALSE,
  no_warnings = TRUE
)

Arguments

expr_mat	single-cell expression matrix or Seurat object
query_genes	A vector or named list of vectors of genesets of interest to compare via GSEA. If supplying a named list, then the gene set names will appear in the output.
cluster_ids	vector of cell cluster assignments, supplied as a vector with order that matches columns in expr_mat. Not required if running per cell.
n_perm	Number of permutation for fgsea function. Defaults to 1000.
per_cell	if true run per cell, otherwise per cluster.
scale	convert expr_mat into zscores prior to running GSEA?, default = FALSE
no_warnings	suppress warnings from gsea ties

Value

dataframe of gsea scores (pval, NES), with clusters as rownames

NCBI-Hackathons/RClusterCT documentation built on Aug. 30, 2024, 2:05 a.m.