Now I'm doing enrichment using clusterprofiler and WebGestalR. In clusterprofiler:
x <- unique(unlist(as.list(org.Bt.egGO2ALLEGS)))
length(x)#5586
there are 5586 genes with GO annotation.
In WebGestalR:
enrichD_BP <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Biological_Process_noRedundant") geneSet_BP <- enrichD_BP$geneSet length(unique(geneSet_BP$gene))#9011
enrichD_CC <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Cellular_Component_noRedundant") geneSet_CC <- enrichD_CC$geneSet length(unique(geneSet_CC$gene))#6224
enrichD_MF <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Molecular_Function_noRedundant") geneSet_MF <- enrichD_MF$geneSet length(unique(geneSet_MF$gene))#7960
geneSet <- unique(c(unique(geneSet_BP$gene),unique(geneSet_CC$gene),unique(geneSet_MF$gene)))
length(geneSet)#10085
There are at least 10085 genes with GO annotation.
WebGestalR has more gene set than clusterprofiler. So which one is the most up to date and same with online GO database? But how to get the gene set from online GO database. This question has puzzled me these days. Becasue I think they two are powerful and should have the same results
thank you for your information. But I can't run this:
Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
do you know why? How can I see the data source for the org.Bt.eg.db package? Thanks
I have soveld this problem. Thanks
But the go-basic.obo file only records go terms, and the structure of subclass, not the gene lists in each term. Do you think it is goa_cow.gaf.gz?