GOAnalysisSave {DAPAR} | R Documentation

## Returns an `MSnSet` object with the results of the GO analysis performed with the functions `enrichGO` and/or `groupGO` of the `clusterProfiler` package.

### Description

This method returns an `MSnSet` object with the results of the Gene Ontology analysis.

### Usage

    GOAnalysisSave(
      obj,
      ggo_res = NULL,
      ego_res = NULL,
      organism,
      ontology,
      levels,
      pvalueCutoff,
      typeUniverse
    )

### Arguments

`obj` | An object of the class `MSnSet`
`ggo_res` | The object returned by the function `group_GO` of the package `DAPAR` or the function `groupGO` of the package `clusterProfiler`
`ego_res` | The object returned by the function `enrich_GO` of the package `DAPAR` or the function `enrichGO` of the package `clusterProfiler`
`organism` | The parameter OrgDb of the functions `bitr`, `groupGO` and `enrichGO`
`ontology` | One of "MF", "BP", and "CC" subontologies
`levels` | A vector of the different GO grouping levels to save
`pvalueCutoff` | The qvalue cutoff (same parameter as in the function `enrichGO` of the package `clusterProfiler`)
`typeUniverse` | The type of background to be used. Values are 'Entire Organism', 'Entire dataset' or 'Custom'. In the latter case, a file should be uploaded by the user

### Value

An object of the class `MSnSet`

### Author(s)

Samuel Wieczorek

[Package DAPAR version 1.24.8 Index]