RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
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ra711 • 0
@ra711-23857
Last seen 24 months ago

Hey everyone I was wondering if anyone has been able to optimize the RDAVIDWebService package to be able to generate a GO Term table with the OFFICIALGENESYMBOL ids instead of working with transcript ids like I used refseqmrna. Please note that the variable resf2adjpval05upreg is just a gene list. Any help is much appreciated!

david <- DAVIDWebService$new(email="myemail@gmail.com",url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/")
ensembl67=useMart(host='may2012.archive.ensembl.org', dataset="mmusculus_gene_ensembl", biomart='ENSEMBL_MART_ENSEMBL')
biomart_f2_adjpval05_upreg <- getBM(attributes=c('refseq_mrna'),filters = 'mgi_symbol', values = res_f2_adjpval05_upreg , mart = ensembl67)
addList(david, biomart_f2_adjpval05_upreg$refseq_mrna, idType="REFSEQ_MRNA",listName="res_f2_adjpval05_upreg", listType="Gene")
write.table(getFunctionalAnnotationChart(david),file="GOTerm_VitDvsNoVitD_Colon_AdjP05_LFCGreaterThan0.txt",sep="\t")
RDAVIDWebService Gene Ontology GOTerm biomaRt • 391 views
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