On Mon, Jul 6, 2009 at 8:33 AM, Vince Schulz <vincent.schulz@yale.edu>wrote:

> I would like to export wig variablestep files using the rtrack package.  I
> get an error if I export files that have "overlapping" features on different
> chromosomes.  For example, I can't export this:
>
> chr1    NimbleScan      CHR01FS000924213        924213  924214
>  -0.192999968716105      .       .       CHR01FS000924213
> chr9    NimbleScan      CHR09FS138569971        924211  924213
>  -0.090919369857934      .       .       CHR09FS138569971
>
> > gffFile <- import.gff("test.gff", version = c("1"), genome = "hg18")
> > export.wig(gffFile, "test.wig", dataFormat = "variableStep")
> Error in export.ucsc(object, con, subformat, ...) :
>  Track not compatible with WIG format: Overlapping features must be on
> separate strands
>
> But I can export
>
> chr1    NimbleScan      CHR01FS000924213        924213  924214
>  -0.192999968716105      .       .       CHR01FS000924213
> chr9    NimbleScan      CHR09FS138569971        924211  924212
>  -0.090919369857934      .       .       CHR09FS138569971
>
> Note 924213 change to 924212 in second working version
>
> Could this be fixed?
>

It probably already was. I suggest updating your packages to the latest
stable release of Bioconductor.

Thanks,
Michael


>
> Thanks,
>
> Vince
>
> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] rtracklayer_1.2.2 RCurl_0.92-0      Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.10.21 grid_2.8.0         IRanges_1.0.14
> lattice_0.17-15
> [5] Matrix_0.999375-16 rJava_0.6-3        XML_1.94-0.1
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

