[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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