Hi, I want to do GO and KEGG analysis using DEGs/Gene IDs to do GSEA and ORA by ClusterProfiler pipeline in R. As my organism (Brassica napus) is not a model plant, so I cant use R supported database such as "org.Ath.eg.db" for Arabidopsis. How can I make my own database i.e., org.Bna.eg.db and then upload in R? I have GO IDs and respective annotations (MF, BP, and CC) that I find directly from another online server using GO IDs.
Hi, I think maybe you'll find this helpful: http://bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html. The R package "AnnotationForge" can be used to create new organism packages for subsequent analysis with ClusterProfiler.
Alternatively, you can use "enricher" function from ClusterProfiler to use manually mapped GO terms to build a enrichResult instance for subsequent analysis. Please refer to: https://rdrr.io/bioc/clusterProfiler/man/enricher.html
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