Dear Steffen, Thank you for your answer, I'll send a suggestion to users at biomart then. In the meantime it's really not a problem indeed, the function "match" enables one to reorder things easily. All the best, Emmanuel On 7 January 2013 21:12, Steffen Durinck <durinck.steffen at="" gene.com=""> wrote: > Hi Emmanuel, > > biomaRt returns you the results as they get passed back from the BioMart > servers and does no reordering. > If you want this changed, this could be a suggestion for the BioMart mailing > list users at biomart.org. > If the order of BioMart server results would be ordered according to the > query input then that would be reflected in the biomaRt results. However > this would complicate queries for example if you have multiple filters then > one would have to start indicating according to which filter results should > be ordered. > > For now I would reorder the output in R if that is what you need. > > Cheers, > Steffen > > On Mon, Jan 7, 2013 at 10:40 AM, Emmanuel Levy <emmanuel.levy at="" gmail.com=""> > wrote: >> >> Hello, >> >> I started using biomaRt and find it really convenient. One thing I >> noticed is that the function getSequence reorders the sequences when >> multiple ids are given as input. >> >> I'm not sure if this is normal or if I missed an option? >> >> Here is what I do: >> >> > ensembl.yeast = useMart(biomart="ensembl", dataset = >> > "scerevisiae_gene_ensembl") >> > ids = c("S000005528","S000000221" ,"S000005993", "S000003105", >> > "S000004200") >> > yeast.gen = getSequence( id=ids, mart=ensembl.yeast, seqType=c("cdna"), >> > type="sgd_transcript" ) >> > yeast.gen[[2]] >> [1] "S000005528" "S000004200" "S000003105" "S000000221" "S000005993" >> >> So the ID No. 5 is now No. 2. It would be convenient if the sequences >> retrieved would be in the order specified by "id". Not that it's a big >> problem but just a thought ... or maybe I missed something? >> >> All the best, >> >> Emmanuel >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >