GOAnalysisSave: Returns an 'MSnSet' object with the results of the GO...

GOAnalysisSaveR 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


samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.