rtracklayer bed import
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@christian-ruckert-3294
Last seen 3.2 years ago
Germany
When trying to import the example .bed track from http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED with the import function from rtracklayer package I get the following error message: > tr = import("example.bed") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 9 elements > sessionInfo() R version 2.10.0 RC (2009-10-18 r50160) x86_64-pc-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.6.0 RCurl_1.3-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] BSgenome_1.14.0 Biobase_2.6.0 Biostrings_2.14.0 IRanges_1.4.0 [5] XML_2.6-0 example.bed: ##Example 5 from Custom Annotation Tracks User's Guide browser position chr7:127471196-127495720 browser hide all track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On" chr7 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0 chr7 127472363 127473530 Pos2 0 + 127472363 127473530 255,0,0 chr7 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0 chr7 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0 chr7 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255 chr7 127477031 127478198 Neg2 0 - 127477031 127478198 0,0,255 chr7 127478198 127479365 Neg3 0 - 127478198 127479365 0,0,255 chr7 127479365 127480532 Pos5 0 + 127479365 127480532 255,0,0 chr7 127480532 127481699 Neg4 0 - 127480532 127481699 0,0,255 Best regards, Christian
Annotation rtracklayer Annotation rtracklayer • 1.6k views
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@michael-lawrence-2759
Last seen 7.9 years ago
On Fri, Oct 30, 2009 at 3:38 AM, Christian Ruckert <cruckert@uni- muenster.de=""> wrote: > When trying to import the example .bed track from > http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED with the > import function from rtracklayer package I get the following error message: > > > tr = import("example.bed") > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > line 1 did not have 9 elements > > The UCSC browser supports so-called "browser lines" at the top of a file which sometimes are a convenient way to pass instructions to the browser upon upload of a track. These are not part of the track data or the BED format. So each line starting with 'browser' should be removed. > > sessionInfo() > R version 2.10.0 RC (2009-10-18 r50160) > x86_64-pc-linux-gnu > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.6.0 RCurl_1.3-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.14.0 Biobase_2.6.0 Biostrings_2.14.0 IRanges_1.4.0 > [5] XML_2.6-0 > > > example.bed: > > ##Example 5 from Custom Annotation Tracks User's Guide > browser position chr7:127471196-127495720 > browser hide all > track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 > itemRgb="On" > chr7 127471196 127472363 Pos1 0 + 127471196 > 127472363 255,0,0 > chr7 127472363 127473530 Pos2 0 + 127472363 > 127473530 255,0,0 > chr7 127473530 127474697 Pos3 0 + 127473530 > 127474697 255,0,0 > chr7 127474697 127475864 Pos4 0 + 127474697 > 127475864 255,0,0 > chr7 127475864 127477031 Neg1 0 - 127475864 > 127477031 0,0,255 > chr7 127477031 127478198 Neg2 0 - 127477031 > 127478198 0,0,255 > chr7 127478198 127479365 Neg3 0 - 127478198 > 127479365 0,0,255 > chr7 127479365 127480532 Pos5 0 + 127479365 > 127480532 255,0,0 > chr7 127480532 127481699 Neg4 0 - 127480532 > 127481699 0,0,255 > > > Best regards, > Christian > > _______________________________________________ > 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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