Question: Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
0
gravatar for endrebak85
12 weeks ago by
endrebak8530
github.com/endrebak/
endrebak8530 wrote:

I want to find the correct background gene list ("universe") to use with ChIPseeker. Ideally I would like to use all the genes that are annotated in GO as the universe for enrichGO and all the genes that are annotated in KEGG for enrichKEGG. Does anyone know how to find these lists? The current way from the docs is to use the gene list from DOSE, but that list contains all genes that have a disease ontology annotation.

chipseeker • 123 views
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by endrebak8530
Answer: Finding the proper universe for enrichGO and enrichKEGG - only the genes that ar
2
gravatar for endrebak85
12 weeks ago by
endrebak8530
github.com/endrebak/
endrebak8530 wrote:
library(org.Hs.eg.db)

df = as.data.frame(org.Hs.egGO)
go_gene_list = unique(sort(df$gene_id))

dfk = as.data.frame(org.Hs.egPATH)
kegg_gene_list = unique(sort(dfk$gene_id))
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by endrebak8530
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