run_gsea {GenomicSuperSignature} | R Documentation

## GSEA on pre-ordered gene lists

### Description

This function is a wrapper of `GSEA` function, making it applicable to a list of gene lists. Set seed for reproducible result.

### Usage

    run_gsea(
      geneList,
      TERM2GENE,
      TERM2NAME,
      minGSSize = 10,
      maxGSSize = 500,
      pvalueCutoff = 0.05,
      verbose = FALSE,
      ...
    )

### Arguments

`geneList` | A list of genes ordered by rank
`TERM2GENE` | User input annotation of TERM TO GENE mapping, a data frame of 2 column with term and gene
`TERM2NAME` | User input of TERM TO NAME mapping, a data.frame of 2 column with term and name. Optional.
`minGSSize` | A mininum size of gene set to be analyzed
`maxGSSize` | A maximum size of gene set to be analyzed
`pvalueCutoff` | p-value cutoff
`verbose` | Logical. Default is `FALSE`
`...` | Any additional argument inherited from `GSEA`.

### Value

A list of `gseaResult` objects. If there is no enrichment result, `NA` will be returned.

[Package GenomicSuperSignature version 1.0.1 Index]