Question: Using wildcard with BiomaRt:getBM
0
gravatar for Daren Tan
10.7 years ago by
Daren Tan160
Daren Tan160 wrote:
Hi, I need to obtain information via biomaRt for all members of interleukin. Trying the following command failed, apparently, getBM doesn't support regexp. I could download all the gene names and filter locally, but this will stress the hosting server and prolong communication time. getBM(attributes=c("hgnc_symbol, "start_position"), filter="hgnc_symbol", values="IL.*", mart=ensembl)
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ADD COMMENTlink modified 10.7 years ago by steffen@stat.Berkeley.EDU600 • written 10.7 years ago by Daren Tan160
Answer: Using wildcard with BiomaRt:getBM
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gravatar for steffen@stat.Berkeley.EDU
10.7 years ago by
Hi Daren, Wildcards don't work. I would query for all genes and then subselect in R. This is not too heavy on the server as it is made for these type of batch queries (you could store the result so you don't have to do it again for a while): ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") ids = getBM(attributes=c("hgnc_symbol","chromosome_name", "start_position"), mart=ensembl) should do it. Cheers, Steffen > > Hi, > > I need to obtain information via biomaRt for all members of interleukin. > Trying the following command failed, apparently, getBM doesn't support > regexp. I could download all the gene names and filter locally, but this > will stress the hosting server and prolong communication time. > > getBM(attributes=c("hgnc_symbol, "start_position"), filter="hgnc_symbol", > values="IL.*", mart=ensembl) > > _______________________________________________ > 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 10.7 years ago by steffen@stat.Berkeley.EDU600
Thanks steffen for the assurance. I will try your suggestion. > Date: Tue, 25 Nov 2008 20:56:31 -0800> Subject: Re: [BioC] Using wildcard with BiomaRt:getBM> From: steffen@stat.Berkeley.EDU> To: daren76@hotmail.com> CC: bioconductor@stat.math.ethz.ch> > Hi Daren,> > Wildcards don't work. I would query for all genes and then subselect in R.> This is not too heavy on the server as it is made for these type of batch> queries (you could store the result so you don't have to do it again for a> while):> > ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")> ids = getBM(attributes=c("hgnc_symbol","chromosome_name",> "start_position"), mart=ensembl)> > > should do it.> > Cheers,> Steffen> > > >> > Hi,> >> > I need to obtain information via biomaRt for all members of interleukin.> > Trying the following command failed, apparently, getBM doesn't support> > regexp. I could download all the gene names and filter locally, but this> > will stress the hosting server and prolong communication time.> >> > getBM(attributes=c("hgnc_symbol, "start_position"), filter="hgnc_symbol",> > values="IL.*", mart=ensembl)> >> > _______________________________________________> > Bioconductor mailing list> > Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives:> > http://news.gmane.org/gmane.science.biology.informatics.conductor> >> _________________________________________________________________ [[elided Hotmail spam]] [[alternative HTML version deleted]]
ADD REPLYlink written 10.7 years ago by Daren Tan160
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