RDAVIDWebService Package Official Gene Symbol IDs in GO Functional Annotation Charts
Entering edit mode
2.1 years ago
ra711 • 0

Blockquote 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 OFFICIAL_GENE_SYMBOL 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$new(email="myemail@gmail.com",url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/") ensembl67=useMart(host='may2012.archive.ensembl.org', dataset="mmusculusgeneensembl", biomart='ENSEMBLMARTENSEMBL') biomartf2adjpval05upreg <- getBM(attributes=c('refseqmrna'),filters = 'mgisymbol', values = resf2adjpval05upreg , mart = ensembl67) addList(david, biomartf2adjpval05upreg$refseqmrna, idType="REFSEQMRNA",listName="resf2adjpval05upreg", listType="Gene") write.table(getFunctionalAnnotationChart(david),file="GOTermVitDvsNoVitDColonAdjP05LFCGreaterThan0.txt",sep="\t")

biomart rdavidwebservice gene ontology goterm R • 595 views

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