Gene ontology categories
In the previous exercise, you tested for enrichment of biological pathways. Now you will test for enrichment in gene sets that are known to influence the same biological process, known as gene ontology (GO) categories. Which GO categories are over-represented in the differentially expressed genes from the leukemia study?
Questo esercizio fa parte del corso
Differential Expression Analysis with limma in R
Istruzioni dell'esercizio
The fitted model object of the leukemia study from Chapter 2, fit2, has been loaded in your workspace. The limma package is already loaded.
Extract the entrez Gene IDs from the data frame
fit2$genes.Test for enriched GO categories with
goana. Set the species to"Hs"for Homo sapiens.View the top 20 enriched GO categories with
topGO. Set the argumentontologyto"BP"to return Biological Processes.
Esercizio pratico interattivo
Prova a risolvere questo esercizio completando il codice di esempio.
# Extract the entrez gene IDs
entrez <- ___
# Test for enriched GO categories
enrich_go <- ___(fit2[1:500, ], geneid = ___, species = ___)
# View the top 20 enriched GO Biological Processes
___(enrich_go, ontology = ___)