GOenrichment: GOenrichment

In askomics/askoR: Differential Expression Analysis using 'edgeR'

GOenrichment

Description

Perform GO enrichment analysis with topGO package. This package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Usage

GOenrichment(resDEG, data_list, parameters, list = NULL, title = NULL)

Arguments

resDEG	data frame contains for each contrast the significance expression (1/0/-1) for all gene.
data_list	list contain all data and metadata (DGEList, samples descriptions, contrast, design and annotations).
parameters	list that contains all arguments charged in Asko_start.
list	gene list of interest if you want to apply GOenrichment function on a specific gene list.
title	name of the gene list if you want to apply GOenrichment function on a specific gene list.

Value

none.

Note

Remember to read the Wiki section in https://github.com/askomics/askoR/wiki

Examples

## Not run: 
   GOenrichment(resDEG, data_list, parameters)
   # OR
   GOenrichment(resDEG, data_list, parameters, list, title)
   # OR
   GOenrichment(resDEG, data_list, parameters, list=NULL, title=NULL)

## End(Not run)

askomics/askoR documentation built on Jan. 17, 2025, 6:23 p.m.