On Mon, Oct 12, 2009 at 1:45 PM, joseph <[email protected]> wrote: > Hello > What do I need to do to SimpleRleList and Rle before I use them to make a > track with export(). > I tried to find help in an earlier thread (WIG from coverage), but I am > still not able to solve the problem. > > > cvge_s_1 > SimpleRleList: 25 elements > names(25): chr1 chr10 chr11 chr12 chr13 chr14 ... chr7 chr8 chr9 chrM chrX > chrY > > cvge_s_1$chr5 > 'integer' Rle instance of length 180857866 with 15165 runs > Lengths: 181838 20 27419 21 25146 21 18711 19 18247 13 ... > Values : 0 1 0 1 0 1 0 1 0 1 ... > > > export(cvge_s_1$chr1, "cvge_s_1_chr1.wig") > #This is what I get for chr1: > track name="R Track" type=wiggle_0 > variableStep chrom=chr1 span=1 > 558223 1 > 558249 1 > 558777 1 > 559783 2 > 559784 3 > ........ > > export(cvge_s_1$chr5, "cvge_s_1_chr5.wig") > #This is what I get for all the other chromosomes; it is always chr1: > > track name="R Track" type=wiggle_0 > chr1 0 4948 0 > chr1 4948 4949 2 > chr1 4949 4950 3 > chr1 4950 4970 4 > chr1 4970 4971 3 > chr1 4971 4972 2 > > Yes, it will always be chromosome 1, because that is the default when creating a RangedData from an Rle. When extracting "chr5" element from the RleList, you're losing the chromosome information. Instead, just subset, e.g. cvge_s_1["chr5"].
> > sessionInfo() > R version 2.10.0 alpha (2009-10-01 r49909) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] HilbertVisGUI_1.3.3 HilbertVis_1.3.4 rtracklayer_1.5.17 > [4] RCurl_1.2-0 bitops_1.0-4.1 ShortRead_1.3.36 > [7] lattice_0.17-25 BSgenome_1.13.16 Biostrings_2.13.48 > [10] IRanges_1.3.87 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.8 hwriter_1.1 tools_2.10.0 XML_2.6-0 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
