Hi, I have a list differentially expressed genes and I wanted to do GO enrichment analysis using topGO. I am having trouble making a geneID2GO annotation file, I extracted GO terms corresponding to each gene ID using the following script. How to make the 'geneID2GO' object from the following script compatible with topGO? Thanks.
library("biomaRt") #collect gene names from biomart mart <- biomaRt::useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host = 'plants.ensembl.org') # Get ensembl gene ids and GO terms GTOGO <- biomaRt::getBM(attributes = c( "ensembl_gene_id", "go_id"), mart = mart) #examine result head (GTOGO) #Remove blank entries GTOGO <- GTOGO[GTOGO$go_id != '',] # convert from table format to list format geneID2GO <- by(GTOGO$go_id, GTOGO$ensembl_gene_id, function(x) as.character(x)) #examine result head (geneID2GO)