runGSEA,PCOSP,data.frame-method {PDATK} | R Documentation

## Run Gene Set Enrichment Analysis On A `PCOSP` Model Object.

### Description

Run Gene Set Enrichment Analysis On A `PCOSP` Model Object.

### Usage

    ## S4 method for signature 'PCOSP,data.frame'
    runGSEA(object, geneSet, numModels, ..., adjMethod = "fdr", allResults = FALSE)

### Arguments

`object` | A `PCOSP` model which has been trained with `trainModel`.
`geneSet` | A `data.frame` with two columns, the first being the name of the gene and the second the gene set. The gene names must match the rownames of `object`. Additional columns will be dropped.
`numModels` | The number of models to use when selecting the top features from the PCOSP model in `object`. If missing will default to the top 10% of models.
`...` | Force subsequent parameters to be named. Not used.
`adjMethod` | An optional parameter specifying the multiple testing correction to use in `piano::runGSAhyper`. This parameter must be named.
`allResults` | Return the full results from `piano::runGSAhyper` instead of a `data.frame` of significant results? Default is FALSE. This parameter must be named.

### Value

A `data.table` containing the significantly enriched gene sets.

[Package PDATK version 1.2.0 Index]