I am trying to improve the way that I am retrieving genes related to a go term, getting something closer to amigo/quickgo (are they the most up to date ?)
I have two simple ways so far:
AnnotationDbi::select(org.Hs.eg.db, keys=go_key, columns = c('SYMBOL'), keytype = "GOALL")
ensembl <- biomaRt::useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") biomaRt::getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id', 'go_id', 'go_linkage_type'), filters = 'go', values = go_key, mart = ensembl)
I kind of like Annotationdbi way better as I have the db on my computer and therefore is it fast, no need to wait for internet request/response.
My first problem is they return slightly different gene list which are also slightly different compare to amigo/quickgo.
Do you know with one is the more updated ? Also I am not sure the GOALL is retrieving all the child and child of child ... maybe I should experiment with recursive method.