Question: how to retrieve data in list using getBM in biomaRt package?
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13.2 years ago by
swang120
swang120 wrote:
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ADD COMMENTlink modified 13.2 years ago by Steffen Durinck580 • written 13.2 years ago by swang120
Answer: how to retrieve data in list using getBM in biomaRt package?
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gravatar for Steffen Durinck
13.2 years ago by
Steffen Durinck580 wrote:
Hi Shiliang, It looks like you forgot to specify the output argument as a list. Try: genelistM <- getBM(attributes = c("entrezgene","go","uniprot_swissprot_accession", "refseq_dna"), filters = "entrezgene",values = ll, mart = mart, na.value =" ", output="list") best, Steffen swang wrote: > Hi,Dr. Durinck: > > > I do need to get a list back from getBM function in biomaRt package, I read > your feedback about getBM when the probe is long. > http://article.gmane.org/gmane.science.biology.informatics.conductor /9172/match=biomart+rmysql+mode > but can you tell me how to get a list back using bomaRt RMySQL mode? > I have a 250 length entrezgene id and try to get back > genelistM <- getBM(attributes = > c("entrezgene","go","uniprot_swissprot_accession", "refseq_dna"), filters = > "entrezgene", > values = ll, mart = mart, na.value = > " ") > > length(ll) > 250 > ll <- getLL(probe,data = "Rosetta") > > I cannot get back in list, otherwise it will tell me wrong. > > Thanks > > Shiliang > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 13.2 years ago by Steffen Durinck580
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