On 07/31/2014 11:41 AM, Valerie Obenchain wrote: > Hi, > > The standard Bioconductor container for sequences are the XString Sorry, the 'BA' below is a typo and should be 'BS'. The BS class is for any long sequence of characters vs the more biologically oriented DNA, RNA and AA types. Valerie > family. BA, DNA, RNA and AA types are supported. See the man page for > details on subsetting and manipulation. > > library(Biostrings) > ?XString > ?DNAString > > You can represent a single sequence > dna <- DNAString("ATGTATCC") >>> dna >> 8-letter "DNAString" instance >> seq: ATGTATCC >>> dna[3] >> 1-letter "DNAString" instance >> seq: G > > or a set of sequences. > dnast <- DNAStringSet(c("AT", "G", "ATC", "C")) >>> dnast >> A DNAStringSet instance of length 4 >> width seq >> [1] 2 AT >> [2] 1 G >> [3] 3 ATC >> [4] 1 C > > Methods for operating on sequences are built on the XString framework, > not Rles. If you really wanted to represent a sequence as an Rle it > would be a character Rle and constructed in the same way the other > atomic types are. See ?Rle. > > rle <- Rle(c("A", "T", "G", "T", "A", "T", "C"), c(rep(1, 6), 2)) >>> rle >> character-Rle of length 8 with 7 runs >> Lengths: 1 1 1 1 1 1 2 >> Values : "A" "T" "G" "T" "A" "T" "C" >>> rle[3] >> character-Rle of length 1 with 1 run >> Lengths: 1 >> Values : "G" > > > Valerie > > > On 07/29/2014 04:04 AM, Asma rabe wrote: >> Hi All, >> >> >> I have a question DNA sequence encoding in Rle objects >> >> >> #------------------------- >> >>> From IRanges vignette >> >> >> the sequence *{*1, 1, 1, 2, 3, 3*} * can be represented as values >> >> = *{*1, 2, 3*}* , run lengths = {3, 1, 2*}* . >> >> >> #--------------------------- >> >> suppose we have a sequence of chr1 from pos 1-8 ATGTATCC. How it >> can be >> as Rle object Rle the so that it is recognized at pos 3 for instance the >> nuceoyide is G for comparison with reference genome? >> >> >> Thank you very much in advance. >> >> [[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 >> > >