run_gsea {clustifyr} | R Documentation

## 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

### Examples

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

[Package clustifyr version 0.99.8 Index]