run_gsea: Run GSEA to compare a gene list(s) to per cell or per cluster...
In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

Description Usage Arguments Value Examples

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

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

`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

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

run_gsea(
    expr_mat = pbmc_matrix_small,
    query_genes = pbmc_vargenes[1:100],
    n_perm = 10,
    cluster_ids = pbmc_meta$classified,
    no_warnings = TRUE
)