Hello Bioconductor curators, How I can merge two subseqs of one DNAStringSet into one DNAStringSet? seq.list=list() seq.list[1]=paste(rep("AT",50),collapse="") seq.list[2]=paste(rep("GC",50),collapse="") example = DNAStringSet(unlist(seq.list)) length(example) = 2 width(example) = 100 start1 = 1 end1 = 20 start2 = 40 end2 = 60 first.subseq = subseq(example,start1,end1) second.subseq = subseq(example,start2,end2) c(first.subseq,second.subseq) doesn´t paste the sequences together Is there an easy method? Or do i have to loop over all entries? Thank you in anticipation Kristian Ullrich Institute of Plant Biochemistry [[alternative HTML version deleted]]

Hi Kristian, To combine all ranges in first.subseq and second.subseq, singleseq <- c(unlist(first.subseq), unlist(second.subseq)) > singleseq 82-letter "DNAString" instance seq: ATATATATATATATATATATGCGCGCGCGCGCGCGC...TATATATATATATATCGCGCGCGCGCGCGCG CGCGC To combine the ranges within first and second and then create a DNAStringSet, here is an approach using unlist and views, seqlist <- list(first.subseq, second.subseq) widths <- sapply(seqlist, function(x) sum(width(x))) seqviews <- successiveViews(singleseq, widths) as(seqviews, "DNAStringSet") A DNAStringSet instance of length 2 width seq [1] 40 ATATATATATATATATATATGCGCGCGCGCGCGCGCGCGC [2] 42 TATATATATATATATATATATCGCGCGCGCGCGCGCGCGCGC Valerie On 06/13/11 04:01, Ullrich, Kristian wrote: > Hello Bioconductor curators, > > How I can merge two subseqs of one DNAStringSet into one DNAStringSet? > > seq.list=list() > seq.list[1]=paste(rep("AT",50),collapse="") > seq.list[2]=paste(rep("GC",50),collapse="") > example = DNAStringSet(unlist(seq.list)) > > length(example) = 2 > width(example) = 100 > start1 = 1 > end1 = 20 > start2 = 40 > end2 = 60 > first.subseq = subseq(example,start1,end1) > second.subseq = subseq(example,start2,end2) > > c(first.subseq,second.subseq) doesn?t paste the sequences together > > Is there an easy method? Or do i have to loop over all entries? > > Thank you in anticipation > > Kristian Ullrich > Institute of Plant Biochemistry > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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