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

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

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

Examples

NULL

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.