Reg. rtracklayer and blocks
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@johannes-waage-3817
Last seen 7.9 years ago
Hi all, Rtracklayer interacts nicely with UCSC GB, but does anyone know if there is support for uploading and displaying BED-tracks with thin and thick lines (e.g. for visualizing splice-junction data from RNA-seq). Is it possible to manipulate thickStart and thickEnd as well as other optional BED-fields? Thanks in advance, JW, Biotech Researh and Innovation Center Uni. of Copenhagen [[alternative HTML version deleted]]
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@michael-lawrence-2759
Last seen 7.9 years ago
On Mon, Nov 23, 2009 at 2:08 AM, Johannes Waage <johannes.waage@gmail.com>wrote: > Hi all, > > Rtracklayer interacts nicely with UCSC GB, but does anyone know if there is > support for uploading and displaying BED-tracks with thin and thick lines > (e.g. for visualizing splice-junction data from RNA-seq). > Is it possible to manipulate thickStart and thickEnd as well as other > optional BED-fields? > > All BED fields are supported. If your RangedData has the thickStart and thickEnd columns, they will be transmitted to the browser, as long as you're using the BED format for the transmission. By default, the format is automatically determined. Basically, BED is only used when there is no numeric score column, otherwise WIG or bedGraph is chosen. To force BED, pass format = "bed" when uploading the track. > Thanks in advance, > > JW, > Biotech Researh and Innovation Center > Uni. of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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Thank you for your reply. Trying to pass blockSizes as a column with i.e. "20,20", disrupts the interaction with UCSC. My RangedData looks like this. RangedData with 24 rows and 9 value columns across 1 space space ranges | itemRgb score name thickStart thickEnd blockCount blockSizes blockStarts strand <character> <iranges> | <character> <numeric> <character> <numeric> <numeric> <numeric> <character> <character> <factor> 1 chr2 [5971505, 5972574] | 0,0,0 1000 Upf2 0 0 2 20,20 0,1049 + 2 chr2 [5872579, 5878536] | 0,0,0 1000 Upf2 0 0 2 20,20 0,5937 + 3 chr2 [5872579, 5955177] | 150,0,0 1000 Upf2 0 0 2 20,20 0,82578 + 4 chr2 [5950571, 5955177] | 0,0,0 1000 Upf2 0 0 2 20,20 0,4586 + 5 chr2 [5872579, 5894534] | 150,0,0 1000 Upf2 0 0 2 20,20 0,21935 + 6 chr2 [5882738, 5894534] | 0,0,0 1000 Upf2 0 0 2 20,20 0,11776 + 7 chr2 [5948514, 5950427] | 0,0,0 1000 Upf2 0 0 2 20,20 0,1893 + 8 chr2 [5947344, 5948278] | 0,0,0 1000 Upf2 0 0 2 20,20 0,914 + 9 chr2 [5961587, 5967963] | 0,0,0 1000 Upf2 0 0 2 20,20 0,6356 + 10 chr2 [5909498, 5924610] | 0,0,0 1000 Upf2 0 0 2 20,20 0,15092 + Removing bockSizes and blockStarts from the object allows upload, but of course doesn't get me what I need. Furthermore, how do I enable colors as per the preamble itemRgb=On in custom tracks? Thank you in advance, Johannes On Mon, Nov 23, 2009 at 3:31 PM, Michael Lawrence <mflawren@fhcrc.org>wrote: > > > On Mon, Nov 23, 2009 at 2:08 AM, Johannes Waage <johannes.waage@gmail.com>wrote: > >> Hi all, >> >> Rtracklayer interacts nicely with UCSC GB, but does anyone know if there >> is >> support for uploading and displaying BED-tracks with thin and thick lines >> (e.g. for visualizing splice-junction data from RNA-seq). >> Is it possible to manipulate thickStart and thickEnd as well as other >> optional BED-fields? >> >> > All BED fields are supported. If your RangedData has the thickStart and > thickEnd columns, they will be transmitted to the browser, as long as you're > using the BED format for the transmission. By default, the format is > automatically determined. Basically, BED is only used when there is no > numeric score column, otherwise WIG or bedGraph is chosen. To force BED, > pass format = "bed" when uploading the track. > > >> Thanks in advance, >> >> JW, >> Biotech Researh and Innovation Center >> Uni. of Copenhagen >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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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On Wed, Nov 25, 2009 at 5:59 AM, Johannes Waage <johannes.waage@gmail.com>wrote: > Thank you for your reply. > > Trying to pass blockSizes as a column with i.e. "20,20", disrupts the > interaction with UCSC. My RangedData looks like this. > > RangedData with 24 rows and 9 value columns across 1 space > space ranges | itemRgb score name > thickStart thickEnd blockCount blockSizes blockStarts strand > <character> <iranges> | <character> <numeric> <character> > <numeric> <numeric> <numeric> <character> <character> <factor> > 1 chr2 [5971505, 5972574] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,1049 + > 2 chr2 [5872579, 5878536] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,5937 + > 3 chr2 [5872579, 5955177] | 150,0,0 1000 > Upf2 0 0 2 20,20 0,82578 + > 4 chr2 [5950571, 5955177] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,4586 + > 5 chr2 [5872579, 5894534] | 150,0,0 1000 > Upf2 0 0 2 20,20 0,21935 + > 6 chr2 [5882738, 5894534] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,11776 + > 7 chr2 [5948514, 5950427] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,1893 + > 8 chr2 [5947344, 5948278] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,914 + > 9 chr2 [5961587, 5967963] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,6356 + > 10 chr2 [5909498, 5924610] | 0,0,0 1000 > Upf2 0 0 2 20,20 0,15092 + > > Removing bockSizes and blockStarts from the object allows upload, but of > course doesn't get me what I need. It seems the confusion here stems from the differences between the IRanges and BED interval bound conventions. Ranges objects are always fully closed intervals, 1-based, while BED is 0-based and half-open. Thus, an adjustment is made for the chromStarts/chromEnds (which become a Ranges object), while no such translation occurs for the textual blockStarts. There is an adjustment when retrieving the blocks as a Ranges object via the blocks() function. In your case, you have correctly specified the blockStarts as 0-based, however the Ranges shown are 1-based and thus will be decremented when passed to UCSC, causing the blocks to extend outside the feature range. I guess rtracklayer needs to adjust those textual blockStarts. Starting to wonder if it wouldn't make more sense to store those numbers as an IntegerList, rather than CSV. > Furthermore, how do I enable colors as per the preamble itemRgb=On in > custom tracks? > > There are several ways. One way: when you upload the track you can specify itemRgb=TRUE. You can also modify the 'trackLine' slot after coercing the RangedData to a UCSCData. > Thank you in advance, > > Johannes > > > On Mon, Nov 23, 2009 at 3:31 PM, Michael Lawrence <mflawren@fhcrc.org>wrote: > >> >> >> On Mon, Nov 23, 2009 at 2:08 AM, Johannes Waage <johannes.waage@gmail.com>> > wrote: >> >>> Hi all, >>> >>> Rtracklayer interacts nicely with UCSC GB, but does anyone know if there >>> is >>> support for uploading and displaying BED-tracks with thin and thick lines >>> (e.g. for visualizing splice-junction data from RNA-seq). >>> Is it possible to manipulate thickStart and thickEnd as well as other >>> optional BED-fields? >>> >>> >> All BED fields are supported. If your RangedData has the thickStart and >> thickEnd columns, they will be transmitted to the browser, as long as you're >> using the BED format for the transmission. By default, the format is >> automatically determined. Basically, BED is only used when there is no >> numeric score column, otherwise WIG or bedGraph is chosen. To force BED, >> pass format = "bed" when uploading the track. >> >> >>> Thanks in advance, >>> >>> JW, >>> Biotech Researh and Innovation Center >>> Uni. of Copenhagen >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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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