Hi Michael and Martin, Views() works great, specially for large chromosomes.
Problem solved. Thank you, Ivan On Wed, Jun 1, 2011 at 12:25 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > > > On Wed, Jun 1, 2011 at 9:06 AM, Ivan Gregoretti <ivang...@gmail.com> wrote: >> >> Hello IRanges connoisseurs, >> >> Is there a function like subseq() but with the ability to accept a >> vector of starts? >> >> >> For instance, if I want to chop the beginning of the murine >> mitochondrial DNA into 50 nucleotides, I'd do >> >> library(BSgenome.Mmusculus.UCSC.mm9) >> >> subseq(Mmusculus[["chrM"]], start=1, width=50) >> subseq(Mmusculus[["chrM"]], start=51, width=50) >> subseq(Mmusculus[["chrM"]], start=101, width=50) >> ... >> >> however, it would be more convenient something like this >> >> subseq(Mmusculus[["chrM"]], start=c(1,51,101), width=50) >> > > So you would expect a DNAStringSet back? That is a little strange: > subsetting a DNAString into a DNAStringSet. Perhaps you really want some way > to "split" the DNAString into pieces. > > In this case, I would suggest using Views. You can use breakIntoChunks in > order to form the ranges component. > > Michael > >> Thank you >> >> Ivan >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing