Ok. That's the obsolete data structure from the chipseq package. If you look at the Rnw for the chipseq vignette, you'll find code for converting one of those into a GRanges, which is now the preferred way of storing that information. I have no recollection of a coerce method from that structure to a RangedData, though one may have existed at some point years ago.
Michael On Mon, Oct 18, 2010 at 8:05 PM, Dario Strbenac <[email protected]>wrote: > Here is a string representation : > > > str(rs) > Formal class 'GenomeData' [package "BSgenome"] with 4 slots > ..@ listData :List of 25 > .. ..$ chr1 :List of 2 > .. .. ..$ -: int [1:375671] 184 191 194 507 511 522 526 545 551 562 ... > .. .. ..$ +: int [1:376001] 152 234 244 248 277 440 450 451 452 458 ... > .. ..$ chr2 :List of 2 > .. .. ..$ -: int [1:331924] 384 392 570 660 716 720 729 731 741 747 ... > .. .. ..$ +: int [1:332302] 234 283 535 590 659 663 682 704 710 724 ... > .. ..$ chr3 :List of 2 > .. .. ..$ -: int [1:212665] 46758 50637 50654 50691 50703 50723 50735 > 50789 54970 55050 ... > .. .. ..$ +: int [1:212274] 38885 50529 50545 50551 50581 50582 50583 > 50630 50695 54859 ... > > ... ... ... > > ..@ elementMetadata: NULL > ..@ elementType : chr "ANY" > ..@ metadata :List of 3 > .. ..$ organism : NULL > .. ..$ provider : NULL > .. ..$ providerVersion: NULL > > ---- Original message ---- > >Date: Mon, 18 Oct 2010 19:48:37 -0700 > >From: Michael Lawrence <[email protected]> > >Subject: Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData > >To: [email protected] > >Cc: [email protected] > > > > That coercion only works if the elements of your > > GenomeData are coercible to RangedData (which after > > coercion are combined into a single RangedData). So > > it would be good to know what's in your GenomeData. > > If each element is a list, as your error message > > suggests, it won't work, as there really is no way > > to convert a list to a RangedData. > > > > Michael > > > > On Mon, Oct 18, 2010 at 7:00 PM, Dario Strbenac > > <[email protected]> wrote: > > > > Hello, > > > > This conversion used to work before but it seems > > like it doesn't any longer. > > > > > summary(rs) > > Length Class Mode > > 25 GenomeData S4 > > > as(rs, "RangedData") > > Error in FUN(X[[1L]], ...) : > > no method or default for coercing "list" to > > "RangedData" > > > sessionInfo() > > R version 2.12.0 (2010-10-15) > > Platform: x86_64-pc-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_Australia.1252 > > LC_CTYPE=English_Australia.1252 > > LC_MONETARY=English_Australia.1252 LC_NUMERIC=C > > [5] LC_TIME=English_Australia.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils > > datasets methods base > > > > other attached packages: > > [1] BSgenome_1.18.0 Biostrings_2.18.0 > > GenomicRanges_1.2.0 IRanges_1.8.0 > > > > loaded via a namespace (and not attached): > > [1] Biobase_2.8.0 > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
