rtracklayer - export.wig issue

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Lavinia Gordon ▴ 480

@lavinia-gordon-2959

Last seen 9.7 years ago

Dear Bioconductors, I am trying to export a RangedData object as a WIG track, but I am getting this error: > wig <- export.wig(B18mtrack, mycon, dataFormat = "auto") 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 > B18mtrack RangedData with 33608 rows and 2 value columns across 1 space space ranges | chr score <character> <iranges> | <character> <numeric> 1 1 [ 15865, 15866] | chr1 0.003188034 2 1 [ 18827, 18828] | chr1 0.013269155 3 1 [ 29407, 29408] | chr1 0.006626525 4 1 [ 29425, 29426] | chr1 0.004264605 5 1 [ 29435, 29436] | chr1 -0.004953431 6 1 [ 69591, 69592] | chr1 0.013326089 7 1 [135252, 135253] | chr1 0.035002515 8 1 [533950, 533951] | chr1 0.002628425 9 1 [534242, 534243] | chr1 0.020180509 ... ... ... ... ... ... 33600 1 [46361270, 46361271] | chr10 0.0051111176 33601 1 [46616291, 46616292] | chr10 -0.0518829821 33602 1 [46762634, 46762635] | chr10 0.0082029002 33603 1 [46762703, 46762704] | chr10 0.0017677983 33604 1 [46763197, 46763198] | chr10 -0.0079985873 33605 1 [46763211, 46763212] | chr10 -0.0001168199 33606 1 [46776799, 46776800] | chr10 0.0929834798 33607 1 [46915981, 46915982] | chr10 -0.0077882567 33608 1 [46951477, 46951478] | chr10 -0.0025202364 However, if I take away the last line of this object, it works: > B18mtrack RangedData with 33607 rows and 2 value columns across 1 space space ranges | chr score <character> <iranges> | <character> <numeric> 1 1 [ 15865, 15866] | chr1 0.003188034 2 1 [ 18827, 18828] | chr1 0.013269155 3 1 [ 29407, 29408] | chr1 0.006626525 4 1 [ 29425, 29426] | chr1 0.004264605 5 1 [ 29435, 29436] | chr1 -0.004953431 6 1 [ 69591, 69592] | chr1 0.013326089 7 1 [135252, 135253] | chr1 0.035002515 8 1 [533950, 533951] | chr1 0.002628425 9 1 [534242, 534243] | chr1 0.020180509 ... ... ... ... ... ... 33599 1 [46344329, 46344330] | chr10 -0.0091757753 33600 1 [46361270, 46361271] | chr10 0.0051111176 33601 1 [46616291, 46616292] | chr10 -0.0518829821 33602 1 [46762634, 46762635] | chr10 0.0082029002 33603 1 [46762703, 46762704] | chr10 0.0017677983 33604 1 [46763197, 46763198] | chr10 -0.0079985873 33605 1 [46763211, 46763212] | chr10 -0.0001168199 33606 1 [46776799, 46776800] | chr10 0.0929834798 33607 1 [46915981, 46915982] | chr10 -0.0077882567 (The .wig file loads perfectly into the UCSC genome browser) Can anyone tell me what is wrong? I thought it might be related to this post: https://stat.ethz.ch/pipermail/bioconductor/2009-July/028470.html but I can't see anything like this in my data. With thanks for your time, Lavinia Gordon. R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.8.9 rtracklayer_1.10.6 RCurl_1.5-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.4 BSgenome_1.18.3 [4] GenomicRanges_1.2.3 XML_3.2-0 -- Senior Bioinformatics Officer Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email

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ADD COMMENT • link updated 13.1 years ago by Michael Lawrence ★ 11k • written 13.1 years ago by Lavinia Gordon ▴ 480

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

On Thu, Mar 31, 2011 at 8:34 PM, Lavinia Gordon <lavinia.gordon@mcri.edu.au>wrote: > Dear Bioconductors, > > I am trying to export a RangedData object as a WIG track, but I am getting > this error: > > wig <- export.wig(B18mtrack, mycon, dataFormat = "auto") > 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 > > B18mtrack > RangedData with 33608 rows and 2 value columns across 1 space > space ranges | chr score > <character> <iranges> | <character> <numeric> > 1 1 [ 15865, 15866] | chr1 0.003188034 > 2 1 [ 18827, 18828] | chr1 0.013269155 > 3 1 [ 29407, 29408] | chr1 0.006626525 > 4 1 [ 29425, 29426] | chr1 0.004264605 > 5 1 [ 29435, 29436] | chr1 -0.004953431 > 6 1 [ 69591, 69592] | chr1 0.013326089 > 7 1 [135252, 135253] | chr1 0.035002515 > 8 1 [533950, 533951] | chr1 0.002628425 > 9 1 [534242, 534243] | chr1 0.020180509 > ... ... ... ... ... ... > 33600 1 [46361270, 46361271] | chr10 0.0051111176 > 33601 1 [46616291, 46616292] | chr10 -0.0518829821 > 33602 1 [46762634, 46762635] | chr10 0.0082029002 > 33603 1 [46762703, 46762704] | chr10 0.0017677983 > 33604 1 [46763197, 46763198] | chr10 -0.0079985873 > 33605 1 [46763211, 46763212] | chr10 -0.0001168199 > 33606 1 [46776799, 46776800] | chr10 0.0929834798 > 33607 1 [46915981, 46915982] | chr10 -0.0077882567 > 33608 1 [46951477, 46951478] | chr10 -0.0025202364 > > However, if I take away the last line of this object, it works: > > B18mtrack > RangedData with 33607 rows and 2 value columns across 1 space > space ranges | chr score > <character> <iranges> | <character> <numeric> > 1 1 [ 15865, 15866] | chr1 0.003188034 > 2 1 [ 18827, 18828] | chr1 0.013269155 > 3 1 [ 29407, 29408] | chr1 0.006626525 > 4 1 [ 29425, 29426] | chr1 0.004264605 > 5 1 [ 29435, 29436] | chr1 -0.004953431 > 6 1 [ 69591, 69592] | chr1 0.013326089 > 7 1 [135252, 135253] | chr1 0.035002515 > 8 1 [533950, 533951] | chr1 0.002628425 > 9 1 [534242, 534243] | chr1 0.020180509 > ... ... ... ... ... ... > 33599 1 [46344329, 46344330] | chr10 -0.0091757753 > 33600 1 [46361270, 46361271] | chr10 0.0051111176 > 33601 1 [46616291, 46616292] | chr10 -0.0518829821 > 33602 1 [46762634, 46762635] | chr10 0.0082029002 > 33603 1 [46762703, 46762704] | chr10 0.0017677983 > 33604 1 [46763197, 46763198] | chr10 -0.0079985873 > 33605 1 [46763211, 46763212] | chr10 -0.0001168199 > 33606 1 [46776799, 46776800] | chr10 0.0929834798 > 33607 1 [46915981, 46915982] | chr10 -0.0077882567 > > (The .wig file loads perfectly into the UCSC genome browser) > > Can anyone tell me what is wrong? > It's hard to say without having your complete dataset. Are you sure none of the ranges are overlapping? What happens if you try just the last 10 ranges? What does this return: isDisjoint(ranges(B18mtrack)$chr10) Thanks, Michael I thought it might be related to this post: > https://stat.ethz.ch/pipermail/bioconductor/2009-July/028470.html > but I can't see anything like this in my data. > > With thanks for your time, > > Lavinia Gordon. > > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.8.9 rtracklayer_1.10.6 RCurl_1.5-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.4 BSgenome_1.18.3 > [4] GenomicRanges_1.2.3 XML_3.2-0 > > > > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australia > www.mcri.edu.au > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD COMMENT • link 13.1 years ago Michael Lawrence ★ 11k

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Hi Michael, Thank you for your reply. I think my object may have been set up incorrectly as your suggested command does not give work on my data. On 2/04/2011 12:08 AM, Michael Lawrence wrote: > > > On Thu, Mar 31, 2011 at 8:34 PM, Lavinia Gordon > <lavinia.gordon@mcri.edu.au <mailto:lavinia.gordon@mcri.edu.au="">> wrote: > > Dear Bioconductors, > > I am trying to export a RangedData object as a WIG track, but I am > getting this error: > > wig <- export.wig(B18mtrack, mycon, dataFormat = "auto") > 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 > > B18mtrack > RangedData with 33608 rows and 2 value columns across 1 space > space ranges | chr score > <character> <iranges> | <character> <numeric> > 1 1 [ 15865, 15866] | chr1 0.003188034 > 2 1 [ 18827, 18828] | chr1 0.013269155 > 3 1 [ 29407, 29408] | chr1 0.006626525 > 4 1 [ 29425, 29426] | chr1 0.004264605 > 5 1 [ 29435, 29436] | chr1 -0.004953431 > 6 1 [ 69591, 69592] | chr1 0.013326089 > 7 1 [135252, 135253] | chr1 0.035002515 > 8 1 [533950, 533951] | chr1 0.002628425 > 9 1 [534242, 534243] | chr1 0.020180509 > ... ... ... ... ... ... > 33600 1 [46361270, 46361271] | chr10 0.0051111176 > 33601 1 [46616291, 46616292] | chr10 -0.0518829821 > 33602 1 [46762634, 46762635] | chr10 0.0082029002 > 33603 1 [46762703, 46762704] | chr10 0.0017677983 > 33604 1 [46763197, 46763198] | chr10 -0.0079985873 > 33605 1 [46763211, 46763212] | chr10 -0.0001168199 > 33606 1 [46776799, 46776800] | chr10 0.0929834798 > 33607 1 [46915981, 46915982] | chr10 -0.0077882567 > 33608 1 [46951477, 46951478] | chr10 -0.0025202364 > > However, if I take away the last line of this object, it works: > > B18mtrack > RangedData with 33607 rows and 2 value columns across 1 space > space ranges | chr score > <character> <iranges> | <character> <numeric> > 1 1 [ 15865, 15866] | chr1 0.003188034 > 2 1 [ 18827, 18828] | chr1 0.013269155 > 3 1 [ 29407, 29408] | chr1 0.006626525 > 4 1 [ 29425, 29426] | chr1 0.004264605 > 5 1 [ 29435, 29436] | chr1 -0.004953431 > 6 1 [ 69591, 69592] | chr1 0.013326089 > 7 1 [135252, 135253] | chr1 0.035002515 > 8 1 [533950, 533951] | chr1 0.002628425 > 9 1 [534242, 534243] | chr1 0.020180509 > ... ... ... ... ... ... > 33599 1 [46344329, 46344330] | chr10 -0.0091757753 > 33600 1 [46361270, 46361271] | chr10 0.0051111176 > 33601 1 [46616291, 46616292] | chr10 -0.0518829821 > 33602 1 [46762634, 46762635] | chr10 0.0082029002 > 33603 1 [46762703, 46762704] | chr10 0.0017677983 > 33604 1 [46763197, 46763198] | chr10 -0.0079985873 > 33605 1 [46763211, 46763212] | chr10 -0.0001168199 > 33606 1 [46776799, 46776800] | chr10 0.0929834798 > 33607 1 [46915981, 46915982] | chr10 -0.0077882567 > > (The .wig file loads perfectly into the UCSC genome browser) > > Can anyone tell me what is wrong? > > > It's hard to say without having your complete dataset. Are you sure > none of the ranges are overlapping? yes > What happens if you try just the last 10 ranges? The wig track loads without problem. > > What does this return: isDisjoint(ranges(B18mtrack)$chr10) > isDisjoint(ranges(B18mtrack)$chr10) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "isDisjoint", for signature "NULL" > ranges(B18mtrack)$chr10 NULL I thought I had followed the examples in the IRanges reference correctly, but I'll go back through and check. Many thanks for your time, Lavinia. > > Thanks, > Michael > > I thought it might be related to this post: > https://stat.ethz.ch/pipermail/bioconductor/2009-July/028470.html > but I can't see anything like this in my data. > > With thanks for your time, > > Lavinia Gordon. > > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.8.9 rtracklayer_1.10.6 RCurl_1.5-0 > bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.4 BSgenome_1.18.3 > [4] GenomicRanges_1.2.3 XML_3.2-0 > > > > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australia > www.mcri.edu.au <http: www.mcri.edu.au=""> > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > > If you have any question, please contact MCRI IT Helpdesk for further > assistance. > ______________________________________________________________________ -- Senior Bioinformatics Officer Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ [[alternative HTML version deleted]]

ADD REPLY • link 13.1 years ago Lavinia Gordon ▴ 480

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On Fri, Apr 1, 2011 at 6:16 PM, Lavinia Gordon <lavinia.gordon@mcri.edu.au>wrote: > Hi Michael, > > Thank you for your reply. I think my object may have been set up > incorrectly as your suggested command does not give work on my data. > > > On 2/04/2011 12:08 AM, Michael Lawrence wrote: > > > > On Thu, Mar 31, 2011 at 8:34 PM, Lavinia Gordon < > lavinia.gordon@mcri.edu.au> wrote: > >> Dear Bioconductors, >> >> I am trying to export a RangedData object as a WIG track, but I am getting >> this error: >> > wig <- export.wig(B18mtrack, mycon, dataFormat = "auto") >> 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 >> > B18mtrack >> RangedData with 33608 rows and 2 value columns across 1 space >> space ranges | chr score >> <character> <iranges> | <character> <numeric> >> 1 1 [ 15865, 15866] | chr1 0.003188034 >> 2 1 [ 18827, 18828] | chr1 0.013269155 >> 3 1 [ 29407, 29408] | chr1 0.006626525 >> 4 1 [ 29425, 29426] | chr1 0.004264605 >> 5 1 [ 29435, 29436] | chr1 -0.004953431 >> 6 1 [ 69591, 69592] | chr1 0.013326089 >> 7 1 [135252, 135253] | chr1 0.035002515 >> 8 1 [533950, 533951] | chr1 0.002628425 >> 9 1 [534242, 534243] | chr1 0.020180509 >> ... ... ... ... ... ... >> 33600 1 [46361270, 46361271] | chr10 0.0051111176 >> 33601 1 [46616291, 46616292] | chr10 -0.0518829821 >> 33602 1 [46762634, 46762635] | chr10 0.0082029002 >> 33603 1 [46762703, 46762704] | chr10 0.0017677983 >> 33604 1 [46763197, 46763198] | chr10 -0.0079985873 >> 33605 1 [46763211, 46763212] | chr10 -0.0001168199 >> 33606 1 [46776799, 46776800] | chr10 0.0929834798 >> 33607 1 [46915981, 46915982] | chr10 -0.0077882567 >> 33608 1 [46951477, 46951478] | chr10 -0.0025202364 >> >> I see the problem now. Your 'chr' column needs to be specified as the 'space' argument to the RangedData constructor. > However, if I take away the last line of this object, it works: >> > B18mtrack >> RangedData with 33607 rows and 2 value columns across 1 space >> space ranges | chr score >> <character> <iranges> | <character> <numeric> >> 1 1 [ 15865, 15866] | chr1 0.003188034 >> 2 1 [ 18827, 18828] | chr1 0.013269155 >> 3 1 [ 29407, 29408] | chr1 0.006626525 >> 4 1 [ 29425, 29426] | chr1 0.004264605 >> 5 1 [ 29435, 29436] | chr1 -0.004953431 >> 6 1 [ 69591, 69592] | chr1 0.013326089 >> 7 1 [135252, 135253] | chr1 0.035002515 >> 8 1 [533950, 533951] | chr1 0.002628425 >> 9 1 [534242, 534243] | chr1 0.020180509 >> ... ... ... ... ... ... >> 33599 1 [46344329, 46344330] | chr10 -0.0091757753 >> 33600 1 [46361270, 46361271] | chr10 0.0051111176 >> 33601 1 [46616291, 46616292] | chr10 -0.0518829821 >> 33602 1 [46762634, 46762635] | chr10 0.0082029002 >> 33603 1 [46762703, 46762704] | chr10 0.0017677983 >> 33604 1 [46763197, 46763198] | chr10 -0.0079985873 >> 33605 1 [46763211, 46763212] | chr10 -0.0001168199 >> 33606 1 [46776799, 46776800] | chr10 0.0929834798 >> 33607 1 [46915981, 46915982] | chr10 -0.0077882567 >> >> (The .wig file loads perfectly into the UCSC genome browser) >> >> Can anyone tell me what is wrong? >> > > It's hard to say without having your complete dataset. Are you sure none of > the ranges are overlapping? > > yes > > What happens if you try just the last 10 ranges? > > The wig track loads without problem. > > > What does this return: isDisjoint(ranges(B18mtrack)$chr10) > > > > isDisjoint(ranges(B18mtrack)$chr10) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "isDisjoint", for > signature "NULL" > > ranges(B18mtrack)$chr10 > NULL > > I thought I had followed the examples in the IRanges reference correctly, > but I'll go back through and check. > > Many thanks for your time, > > Lavinia. > > > > Thanks, > Michael > > I thought it might be related to this post: >> https://stat.ethz.ch/pipermail/bioconductor/2009-July/028470.html >> but I can't see anything like this in my data. >> >> With thanks for your time, >> >> Lavinia Gordon. >> >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] IRanges_1.8.9 rtracklayer_1.10.6 RCurl_1.5-0 >> bitops_1.0-4.1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.10.0 Biostrings_2.18.4 BSgenome_1.18.3 >> [4] GenomicRanges_1.2.3 XML_3.2-0 >> >> >> >> >> -- >> Senior Bioinformatics Officer >> Murdoch Childrens Research Institute >> Royal Children's Hospital >> Flemington Road >> Parkville >> Victoria 3052 >> Australia >> www.mcri.edu.au >> >> >> ______________________________________________________________________ >> This email has been scanned by the MessageLabs Email Security System. >> For more information please visit http://www.messagelabs.com/email >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > > If you have any question, please contact MCRI IT Helpdesk for further > assistance. > ______________________________________________________________________ > > > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australiawww.mcri.edu.au > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ > [[alternative HTML version deleted]]

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