RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
0
0
Entering edit mode
ra711 • 0
@ra711-23857
Last seen 4.1 years 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 • 928 views
ADD COMMENT

Login before adding your answer.

Traffic: 639 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6