Hi Nicolas -- Nicolas Delhomme <[email protected]> writes:
> Hi all, > > Well the question is quite easy :-) What does this slot holds? Because > it looks very different from the actual positions: i.e. > > these are the 10 first ranges > > > sread(aln.clean[chromosome(aln.clean)=="2R"])@ranges[1:10] It's internal to the way reads themselves are stored. sread(aln.clean) returns a DNAStringSet object, the ranges slot of a DNAStringSet points to offsets into a larger DNAString. As you show later, you want to use position(aln.clean) for alignment information. This representation is meant to be entirely internal to the class. The intention is that the user manipulate objects with defined functions and methods (like position()). Of course the user can get at the contents of slots with @, but there are no guarantees about what will be there if the user does this!. Martin > IRanges object: > start end width > [1] 4141 4176 36 > [2] 4177 4212 36 > [3] 4357 4392 36 > [4] 4465 4500 36 > [5] 5113 5148 36 > [6] 5365 5400 36 > [7] 5401 5436 36 > [8] 6049 6084 36 > [9] 6301 6336 36 > [10] 6373 6408 36 > > and these are the 10 first positions > > >position(aln.clean[chromosome(aln.clean)=="2R"])[1:10] > [1] 6419544 18694365 10064416 17228214 5850736 11976428 15335440 > 3370962 > [9] 15327509 3366816 > > > sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE = en_US .UTF -8 > ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 > ;LC_COLLATE = en_US .UTF -8 > ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8 > ;LC_PAPER = en_US .UTF -8 > ;LC_NAME = C ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.2.0 lattice_0.17-22 BSgenome_1.12.0 > Biostrings_2.12.1 > [5] IRanges_1.2.1 rtracklayer_1.4.0 RCurl_0.94-1 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.1 grid_2.9.0 hwriter_1.1 tools_2.9.0 XML_2.3-0 > > And is there an easy way to create a RangesList from an AlignedRead > object? I figured out how to do it, but I just want to be sure that I > didn't miss it. If it doesn't exist, I think it would be a valuable > addition and I could contribute the few lines of code. > > Best, > > --------------------------------------------------------------- > Nicolas Delhomme > > High Throughput Functional Genomics Center > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8426 > Email: [email protected] > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
