Hi All, this should be an easy question and answer, it is mostly about the best way to do this with the Bioconductor S4 classes. I have a pairwise alignment: A and I want a function which maps from a position in the original sequence (either subject: s, or pattern: p) to the position in the aignment. Essentially, I want a function that looks like: subject alignment 1 1 2 2 3 4 4 5 alignmentPosition(i, which = c("subject", "pattern")), i in 1:length(s) => j in 1:length(alignment) If I had just characters, it would be easy, but since I have objects of type: PairwiseAlignedFixedSubject, I am slightly overwhelmed by the class hierarchy, and the best way to do this. thanks, jim

Jim, Table 3 (Functions for AlignedXString and QualityAlignedXString objects) in Biostrings' Pairwise Alignment vignette http://bioconductor.org/packages/2.5/bioc/vignettes/Biostrings/inst/do c/Alignments.pdf lists some helper functions that may be of use to you. A PairwiseAlignedFixedSubject object has two slots, one for the pattern and one for the subject, to house AlignedXStringSet objects These objects should contain the information you are looking for. In particular, I think myalign <- pairwiseAlignment(...) start(subject(myalign)) should do the trick. Patrick James Bullard wrote: > Hi All, > > this should be an easy question and answer, it is mostly about the > best way to do this with the Bioconductor S4 classes. I have a > pairwise alignment: A and I want a function which maps from a position > in the original sequence (either subject: s, or pattern: p) to the > position in the aignment. Essentially, I want a function that looks like: > > subject alignment > 1 1 > 2 2 > 3 4 > 4 5 > > alignmentPosition(i, which = c("subject", "pattern")), i in > 1:length(s) => j in 1:length(alignment) > > If I had just characters, it would be easy, but since I have objects > of type: PairwiseAlignedFixedSubject, I am slightly overwhelmed by the > class hierarchy, and the best way to do this. > > thanks, jim > > _______________________________________________ > 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