Gene Functional Enrichment analysis

Question

[Bioinf_Questions]

Hello everyone. I'm trying to make a Functional Enrichment BarPlot for my differencial expression analysis, but I'm having trouble with the packages I'm trying to use. What does the input file for the enrichGO function from ClusterProfiler must look like? My organism is soybean, The exemple below is what is shown in the in R's "help".

   data(geneList, package = "DOSE")
de <- names(geneList)[1:100]
yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)

When I try to enter my data (I tried both only the gene IDs and all Deseq2 data) but I keep getting the mesage below, even thought my data was properly imported and even shows using the command "head". Also, what is the soybean "code" to substitute "org.Hs.eg.db"?

Warning message: In data(diff_genes) : data set ‘diff_genes’ not found

Thanks for any help

[jv]

What does the input file for the enrichGO function from ClusterProfiler must look like?

geneList should be a vector of gene ids, not a data.frame, not a list.

Also, what is the soybean "code" to substitute "org.Hs.eg.db"?

I don't see a corresponding genome wide annotation package for Soybean like there is for human, but that's ok. You can use the enricher function in place of enrichGO which will allow you to define your gene sets using the TERM2GENE and TERM2NAME parameters. enrichGO is just a wrapper of sorts for enricher which is meant to streamline GO term enrichment when all the necessary info is conveniently provided in the form of a Bioconductor organism-specific genome wide annotation package.

[Bioinf_Questions]

Thank you. I'll try that.