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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
