Run GSEA to compare a gene list(s) to per cell or per cluster expression data
Source:R/run_fgsea.R
run_gsea.RdUse 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