[BioC] meet problem when use rtracklayer

Yanchun Bao Yanchun.Bao at brunel.ac.uk
Thu Jun 9 16:22:42 CEST 2011


>library(rtracklayer) 
>library(IRanges) 
>library(GenomicRanges) 
>GSMCBPT0<-import.wig("GSM525265_CBP_T0.wig") 
> head(GSMCBPT0) 
UCSCData with 6 rows and 1 value column across 24 spaces
     space           ranges |     score
  <factor>        <IRanges> | <integer>
1    chr11 [165900, 165900] |         2
2    chr11 [165901, 165901] |         2
3    chr11 [165902, 165902] |         2
4    chr11 [165903, 165903] |         2
5    chr11 [165904, 165904] |         2
6    chr11 [165905, 165905] |         2
>targetTrack<-with(GSMCBPT0, GSMCBPT0$scores) ## Not sure if I use it correct 
> session <- browserSession("UCSC") 
> session$targets<-targetTrack 
Error in FUN(X[[1L]], ...) : Invalid chromosomes for hg19: 1 
> export(targetTrack, "tragets.wig") Error in export.ucsc(object, con, 
subformat, append, ...) : Track not compatible with WIG/bedGraph: Overlapping 
features must be on separate strands and every feature width must be positive


     I have a wig file data and I read it by import, then I want to use GCSC 
Genome Browser, I have meet some problems in track and export (follow the 
example of paper Bioinformatics 2009 1841-1842). I am wondering if I use the 
wrong 'with' command? I have no idea, could anybody help me? Thank you very 
much.



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