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

In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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

DAPAR documentation built on April 11, 2021, 6 p.m.