rtrack export.wig
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Vince Schulz ▴ 130
@vince-schulz-3553
Last seen 7 months ago
United States
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? 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
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@michael-lawrence-2759
Last seen 8.0 years ago
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]]
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