>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.

sorry for delay in responding. geo is down at the moment so i can't reproduce your code exactly. but see below On Thu, Jun 9, 2011 at 10:22 AM, Yanchun Bao <yanchun.bao at="" brunel.ac.uk=""> wrote: >>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$scores) ## Not sure if I use it correct above cannot be as intended because "scores" is not an element of GSMCBPT0. anyway, the example involving "with()" in the paper is converting a _data frame_ instance to a RangedData. you already have, as a result of the import, a UCSCData instance GSMCBPT0, which inherits from RangedData >> session <- browserSession("UCSC") >> session$targets<-targetTrack at this point in principle you could use session$targets = GSMCBPT0 > Error in FUN(X[[1L]], ...) : Invalid chromosomes for hg19: 1 what is the result of table(space(GSMCBPT0)) you did not give sessionInfo() so I am not clear on >> 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 it is not clear how you got here. when geo is back up i will try to have a look at this specific wig file. please read the posting guide, try to give full unedited transcript of your commands, and give sessionInfo() result > > > ? ? 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >