IRanges merging query
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@vishal-thapar-3427
Last seen 10.2 years ago
Hi All, I have a question about how to merge / have a union of 2 RangeData objects Say I have a rangeData1 head(rangeData1) RangedData with 6 rows and 0 value columns across 25 spaces space ranges | <character> <iranges> | 1 chr1 [ 101, 283] | 2 chr1 [ 704, 710] | 3 chr1 [ 310, 450] | 4 chr2 [ 582, 635] | 5 chr3 [ 422, 548] | 6 chr4 [ 40, 128] | and another head(rangeData2) RangedData with 6 rows and 0 value columns across 25 spaces space ranges | <character> <iranges> | 1 chr1 [ 90, 200] | 2 chr1 [ 600, 650] | 3 chr1 [ 306, 384] | 4 chr2 [ 650, 690] | 5 chr3 [ 315, 697] | 6 chr5 [ 140, 228] | Would it be possible to merge these two so that I get something like this: RangeData3 RangedData with 7 rows and 0 value columns across 25 spaces space ranges | <character> <iranges> | 1 chr1 [ 90, 283] | 2 chr1 [ 600, 710] | 3 chr1 [ 306, 450] | 4 chr2 [ 582, 690] | 5 chr3 [ 315, 697] | 6 chr4 [ 40, 128] | 7 chr5 [ 140, 228] | Thanks for the help! Sincerely, Vishal [[alternative HTML version deleted]]
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@kasper-daniel-hansen-2979
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ir1, ir2 are your IRanges do reduce(c(ir1, ir2)) Kasper On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar <vishalthapar at="" gmail.com=""> wrote: > Hi All, > > I have a question about how to merge / have a union of 2 RangeData objects > Say I have a rangeData1 > head(rangeData1) > RangedData with 6 rows and 0 value columns across 25 spaces > ? ? ? ?space ? ? ? ? ? ? ranges | > ?<character> ? ? ? ? ?<iranges> | > 1 ? ? ? ? ? chr1 [ ? ?101, ? ? 283] | > 2 ? ? ? ? ? chr1 [ ? ?704, ? ? 710] | > 3 ? ? ? ? ? chr1 [ ? ?310, ? ? 450] | > 4 ? ? ? ? ? chr2 [ ? ?582, ? ? 635] | > 5 ? ? ? ? ? chr3 [ ? ?422, ? ? 548] | > 6 ? ? ? ? ? chr4 [ ? ? ?40, ?128] | > > and another > > head(rangeData2) > RangedData with 6 rows and 0 value columns across 25 spaces > ? ? ? ?space ? ? ? ? ? ? ranges | > ?<character> ? ? ? ? ?<iranges> | > 1 ? ? ? ? ? chr1 [ ? ?90, ? ? 200] | > 2 ? ? ? ? ? chr1 [ ? ?600, ?650] | > 3 ? ? ? ? ? chr1 [ ? ?306, ?384] | > 4 ? ? ? ? ? chr2 [ ? ?650, ? 690] | > 5 ? ? ? ? ? chr3 [ ? ?315, ? 697] | > 6 ? ? ? ? ? chr5 [ ? ?140, ? 228] | > > Would it be possible to merge these two so that I get something like this: > RangeData3 > RangedData with 7 rows and 0 value columns across 25 spaces > ? ? ? ?space ? ? ? ? ? ? ranges | > ?<character> ? ? ? ? ?<iranges> | > 1 ? ? ? ? ? chr1 [ ? ?90, ? ? 283] | > 2 ? ? ? ? ? chr1 [ ? ?600, ?710] | > 3 ? ? ? ? ? chr1 [ ? ?306, ?450] | > 4 ? ? ? ? ? chr2 [ ? ?582, ? 690] | > 5 ? ? ? ? ? chr3 [ ? ?315, ? 697] | > 6 ? ? ? ? ? chr4 [ ? ? ?40, ?128] | > 7 ? ? ? ? ? chr5 [ ? ?140, ? 228] | > > > Thanks for the help! > > Sincerely, > > Vishal > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi Kasper, Thank you for replying back. I had tried this earlier, but what I get is not what I expected. I sort of wanted to "merge" the ranges for each "chr" value. So I want to ranges in Chr1 to be merged separately from Chr2 and so on. What I Get is: > abc.chr=c("chr1","chr1","chr1","chr2","chr3","chr4") > abc.start=c(101,704,310,582,422,40) > abc.end = c(283,710,450,635,548,128) > > def.chr=c("chr1","chr1","chr1","chr2","chr3","chr5") > def.start=c(90,600,306,650,315,140) > def.end=c(200,650,384,690,697,228) > > I1 <- IRanges(start = abc.start, end = abc.end, names=abc.chr) > I2<- IRanges(start = def.start, end = def.end, names=def.chr) > > I1 IRanges of length 6 start end width names [1] 101 283 183 chr1 [2] 704 710 7 chr1 [3] 310 450 141 chr1 [4] 582 635 54 chr2 [5] 422 548 127 chr3 [6] 40 128 89 chr4 > I2 IRanges of length 6 start end width names [1] 90 200 111 chr1 [2] 600 650 51 chr1 [3] 306 384 79 chr1 [4] 650 690 41 chr2 [5] 315 697 383 chr3 [6] 140 228 89 chr5 > > xyz<- reduce(c(I1,I2)) > xyz IRanges of length 3 start end width [1] 40 283 244 [2] 306 697 392 [3] 704 710 7 What I would like is : xyz IRanges of length 7 start end width names [1] 90 283 194 chr1 [2] 600 710 111 chr1 [3] 306 450 145 chr1 [4] 582 690 108 chr2 [5] 315 697 383 chr3 [6] 40 128 89 chr4 [7] 140 228 89 chr5 This doesn't take the "names" into account while reducing / merging. Is there a way to have that taken into account while merging? Thanks again for your help. -vishal On Fri, Nov 12, 2010 at 2:55 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > ir1, ir2 are your IRanges > > do > reduce(c(ir1, ir2)) > > Kasper > > On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar <vishalthapar@gmail.com> > wrote: > > Hi All, > > > > I have a question about how to merge / have a union of 2 RangeData > objects > > Say I have a rangeData1 > > head(rangeData1) > > RangedData with 6 rows and 0 value columns across 25 spaces > > space ranges | > > <character> <iranges> | > > 1 chr1 [ 101, 283] | > > 2 chr1 [ 704, 710] | > > 3 chr1 [ 310, 450] | > > 4 chr2 [ 582, 635] | > > 5 chr3 [ 422, 548] | > > 6 chr4 [ 40, 128] | > > > > and another > > > > head(rangeData2) > > RangedData with 6 rows and 0 value columns across 25 spaces > > space ranges | > > <character> <iranges> | > > 1 chr1 [ 90, 200] | > > 2 chr1 [ 600, 650] | > > 3 chr1 [ 306, 384] | > > 4 chr2 [ 650, 690] | > > 5 chr3 [ 315, 697] | > > 6 chr5 [ 140, 228] | > > > > Would it be possible to merge these two so that I get something like > this: > > RangeData3 > > RangedData with 7 rows and 0 value columns across 25 spaces > > space ranges | > > <character> <iranges> | > > 1 chr1 [ 90, 283] | > > 2 chr1 [ 600, 710] | > > 3 chr1 [ 306, 450] | > > 4 chr2 [ 582, 690] | > > 5 chr3 [ 315, 697] | > > 6 chr4 [ 40, 128] | > > 7 chr5 [ 140, 228] | > > > > > > Thanks for the help! > > > > Sincerely, > > > > Vishal > > > > [[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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Hi Vishal, I think you want to do pairwise union. You can use punion() for this. Cheers, H. On 11/12/2010 12:18 PM, Vishal Thapar wrote: > Hi Kasper, > > Thank you for replying back. I had tried this earlier, but what I get is not > what I expected. I sort of wanted to "merge" the ranges for each "chr" > value. So I want to ranges in Chr1 to be merged separately from Chr2 and so > on. What I Get is: > >> abc.chr=c("chr1","chr1","chr1","chr2","chr3","chr4") >> abc.start=c(101,704,310,582,422,40) >> abc.end = c(283,710,450,635,548,128) >> >> def.chr=c("chr1","chr1","chr1","chr2","chr3","chr5") >> def.start=c(90,600,306,650,315,140) >> def.end=c(200,650,384,690,697,228) >> >> I1<- IRanges(start = abc.start, end = abc.end, names=abc.chr) >> I2<- IRanges(start = def.start, end = def.end, names=def.chr) >> >> I1 > IRanges of length 6 > start end width names > [1] 101 283 183 chr1 > [2] 704 710 7 chr1 > [3] 310 450 141 chr1 > [4] 582 635 54 chr2 > [5] 422 548 127 chr3 > [6] 40 128 89 chr4 >> I2 > IRanges of length 6 > start end width names > [1] 90 200 111 chr1 > [2] 600 650 51 chr1 > [3] 306 384 79 chr1 > [4] 650 690 41 chr2 > [5] 315 697 383 chr3 > [6] 140 228 89 chr5 >> >> xyz<- reduce(c(I1,I2)) >> xyz > IRanges of length 3 > start end width > [1] 40 283 244 > [2] 306 697 392 > [3] 704 710 7 > > > What I would like is : > xyz > IRanges of length 7 > start end width names > [1] 90 283 194 chr1 > [2] 600 710 111 chr1 > [3] 306 450 145 chr1 > [4] 582 690 108 chr2 > [5] 315 697 383 chr3 > [6] 40 128 89 chr4 > [7] 140 228 89 chr5 > > > This doesn't take the "names" into account while reducing / merging. Is > there a way to have that taken into account while merging? > > Thanks again for your help. > > -vishal > > On Fri, Nov 12, 2010 at 2:55 PM, Kasper Daniel Hansen< > kasperdanielhansen at gmail.com> wrote: > >> ir1, ir2 are your IRanges >> >> do >> reduce(c(ir1, ir2)) >> >> Kasper >> >> On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar<vishalthapar at="" gmail.com=""> >> wrote: >>> Hi All, >>> >>> I have a question about how to merge / have a union of 2 RangeData >> objects >>> Say I have a rangeData1 >>> head(rangeData1) >>> RangedData with 6 rows and 0 value columns across 25 spaces >>> space ranges | >>> <character> <iranges> | >>> 1 chr1 [ 101, 283] | >>> 2 chr1 [ 704, 710] | >>> 3 chr1 [ 310, 450] | >>> 4 chr2 [ 582, 635] | >>> 5 chr3 [ 422, 548] | >>> 6 chr4 [ 40, 128] | >>> >>> and another >>> >>> head(rangeData2) >>> RangedData with 6 rows and 0 value columns across 25 spaces >>> space ranges | >>> <character> <iranges> | >>> 1 chr1 [ 90, 200] | >>> 2 chr1 [ 600, 650] | >>> 3 chr1 [ 306, 384] | >>> 4 chr2 [ 650, 690] | >>> 5 chr3 [ 315, 697] | >>> 6 chr5 [ 140, 228] | >>> >>> Would it be possible to merge these two so that I get something like >> this: >>> RangeData3 >>> RangedData with 7 rows and 0 value columns across 25 spaces >>> space ranges | >>> <character> <iranges> | >>> 1 chr1 [ 90, 283] | >>> 2 chr1 [ 600, 710] | >>> 3 chr1 [ 306, 450] | >>> 4 chr2 [ 582, 690] | >>> 5 chr3 [ 315, 697] | >>> 6 chr4 [ 40, 128] | >>> 7 chr5 [ 140, 228] | >>> >>> >>> Thanks for the help! >>> >>> Sincerely, >>> >>> Vishal >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Thanks Herve'. That comes the closest to the answer but it still misses the values for which there is no pair on one of the sets. This is what I get: > punion(I1,I2) Error in .local(x, y, ...) : some pair of ranges have a gap within the 2 members of the pair. Use 'fill.gap=TRUE' to enforce their union by filling the gap. > > punion(I1,I2, fill.gap=TRUE) IRanges of length 6 start end width names [1] 90 283 194 chr1 [2] 600 710 111 chr1 [3] 306 450 145 chr1 [4] 582 690 109 chr2 [5] 315 697 383 chr3 [6] 40 228 189 chr4 The last one is still missing. Any suggestions? -v 2010/11/12 Hervé Pagès <hpages@fhcrc.org> > Hi Vishal, > > I think you want to do pairwise union. You can use punion() for this. > > Cheers, > H. > > > > On 11/12/2010 12:18 PM, Vishal Thapar wrote: > >> Hi Kasper, >> >> Thank you for replying back. I had tried this earlier, but what I get is >> not >> what I expected. I sort of wanted to "merge" the ranges for each "chr" >> value. So I want to ranges in Chr1 to be merged separately from Chr2 and >> so >> on. What I Get is: >> >> abc.chr=c("chr1","chr1","chr1","chr2","chr3","chr4") >>> abc.start=c(101,704,310,582,422,40) >>> abc.end = c(283,710,450,635,548,128) >>> >>> def.chr=c("chr1","chr1","chr1","chr2","chr3","chr5") >>> def.start=c(90,600,306,650,315,140) >>> def.end=c(200,650,384,690,697,228) >>> >>> I1<- IRanges(start = abc.start, end = abc.end, names=abc.chr) >>> I2<- IRanges(start = def.start, end = def.end, names=def.chr) >>> >>> I1 >>> >> IRanges of length 6 >> start end width names >> [1] 101 283 183 chr1 >> [2] 704 710 7 chr1 >> [3] 310 450 141 chr1 >> [4] 582 635 54 chr2 >> [5] 422 548 127 chr3 >> [6] 40 128 89 chr4 >> >>> I2 >>> >> IRanges of length 6 >> start end width names >> [1] 90 200 111 chr1 >> [2] 600 650 51 chr1 >> [3] 306 384 79 chr1 >> [4] 650 690 41 chr2 >> [5] 315 697 383 chr3 >> [6] 140 228 89 chr5 >> >>> >>> xyz<- reduce(c(I1,I2)) >>> xyz >>> >> IRanges of length 3 >> start end width >> [1] 40 283 244 >> [2] 306 697 392 >> [3] 704 710 7 >> >> >> What I would like is : >> xyz >> IRanges of length 7 >> start end width names >> [1] 90 283 194 chr1 >> [2] 600 710 111 chr1 >> [3] 306 450 145 chr1 >> [4] 582 690 108 chr2 >> [5] 315 697 383 chr3 >> [6] 40 128 89 chr4 >> [7] 140 228 89 chr5 >> >> >> This doesn't take the "names" into account while reducing / merging. Is >> there a way to have that taken into account while merging? >> >> Thanks again for your help. >> >> -vishal >> >> On Fri, Nov 12, 2010 at 2:55 PM, Kasper Daniel Hansen< >> kasperdanielhansen@gmail.com> wrote: >> >> ir1, ir2 are your IRanges >>> >>> do >>> reduce(c(ir1, ir2)) >>> >>> Kasper >>> >>> On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar<vishalthapar@gmail.com> >>> wrote: >>> >>>> Hi All, >>>> >>>> I have a question about how to merge / have a union of 2 RangeData >>>> >>> objects >>> >>>> Say I have a rangeData1 >>>> head(rangeData1) >>>> RangedData with 6 rows and 0 value columns across 25 spaces >>>> space ranges | >>>> <character> <iranges> | >>>> 1 chr1 [ 101, 283] | >>>> 2 chr1 [ 704, 710] | >>>> 3 chr1 [ 310, 450] | >>>> 4 chr2 [ 582, 635] | >>>> 5 chr3 [ 422, 548] | >>>> 6 chr4 [ 40, 128] | >>>> >>>> and another >>>> >>>> head(rangeData2) >>>> RangedData with 6 rows and 0 value columns across 25 spaces >>>> space ranges | >>>> <character> <iranges> | >>>> 1 chr1 [ 90, 200] | >>>> 2 chr1 [ 600, 650] | >>>> 3 chr1 [ 306, 384] | >>>> 4 chr2 [ 650, 690] | >>>> 5 chr3 [ 315, 697] | >>>> 6 chr5 [ 140, 228] | >>>> >>>> Would it be possible to merge these two so that I get something like >>>> >>> this: >>> >>>> RangeData3 >>>> RangedData with 7 rows and 0 value columns across 25 spaces >>>> space ranges | >>>> <character> <iranges> | >>>> 1 chr1 [ 90, 283] | >>>> 2 chr1 [ 600, 710] | >>>> 3 chr1 [ 306, 450] | >>>> 4 chr2 [ 582, 690] | >>>> 5 chr3 [ 315, 697] | >>>> 6 chr4 [ 40, 128] | >>>> 7 chr5 [ 140, 228] | >>>> >>>> >>>> Thanks for the help! >>>> >>>> Sincerely, >>>> >>>> Vishal >>>> >>>> [[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]] >> >> _______________________________________________ >> 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 >> > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- *Vishal Thapar, Ph.D.* *Scientific informatics Analyst Cold Spring Harbor Lab Quick Bldg, Lowe Lab 1 Bungtown Road Cold Spring Harbor, NY - 11724* [[alternative HTML version deleted]]
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On Fri, Nov 12, 2010 at 12:18 PM, Vishal Thapar <vishalthapar@gmail.com>wrote: > Hi Kasper, > > Thank you for replying back. I had tried this earlier, but what I get is > not > what I expected. I sort of wanted to "merge" the ranges for each "chr" > value. So I want to ranges in Chr1 to be merged separately from Chr2 and so > on. What I Get is: > > > abc.chr=c("chr1","chr1","chr1","chr2","chr3","chr4") > > abc.start=c(101,704,310,582,422,40) > > abc.end = c(283,710,450,635,548,128) > > > > def.chr=c("chr1","chr1","chr1","chr2","chr3","chr5") > > def.start=c(90,600,306,650,315,140) > > def.end=c(200,650,384,690,697,228) > > > > I1 <- IRanges(start = abc.start, end = abc.end, names=abc.chr) > > I2<- IRanges(start = def.start, end = def.end, names=def.chr) > > > > I1 > IRanges of length 6 > start end width names > [1] 101 283 183 chr1 > [2] 704 710 7 chr1 > [3] 310 450 141 chr1 > [4] 582 635 54 chr2 > [5] 422 548 127 chr3 > [6] 40 128 89 chr4 > > I2 > IRanges of length 6 > start end width names > [1] 90 200 111 chr1 > [2] 600 650 51 chr1 > [3] 306 384 79 chr1 > [4] 650 690 41 chr2 > [5] 315 697 383 chr3 > [6] 140 228 89 chr5 > > > > xyz<- reduce(c(I1,I2)) > > xyz > IRanges of length 3 > start end width > [1] 40 283 244 > [2] 306 697 392 > [3] 704 710 7 > > > What I would like is : > xyz > IRanges of length 7 > start end width names > [1] 90 283 194 chr1 > [2] 600 710 111 chr1 > [3] 306 450 145 chr1 > [4] 582 690 108 chr2 > [5] 315 697 383 chr3 > [6] 40 128 89 chr4 > [7] 140 228 89 chr5 > > > This doesn't take the "names" into account while reducing / merging. Is > there a way to have that taken into account while merging? > > Yes, RangedData takes that into account. So you could do reduce(rbind(rangedData1, rangedData2)) To get out a RangedData of your merged ranges. Btw, Kasper's code works for GRanges but not IRanges. > Thanks again for your help. > > -vishal > > On Fri, Nov 12, 2010 at 2:55 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com> wrote: > > > ir1, ir2 are your IRanges > > > > do > > reduce(c(ir1, ir2)) > > > > Kasper > > > > On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar <vishalthapar@gmail.com> > > wrote: > > > Hi All, > > > > > > I have a question about how to merge / have a union of 2 RangeData > > objects > > > Say I have a rangeData1 > > > head(rangeData1) > > > RangedData with 6 rows and 0 value columns across 25 spaces > > > space ranges | > > > <character> <iranges> | > > > 1 chr1 [ 101, 283] | > > > 2 chr1 [ 704, 710] | > > > 3 chr1 [ 310, 450] | > > > 4 chr2 [ 582, 635] | > > > 5 chr3 [ 422, 548] | > > > 6 chr4 [ 40, 128] | > > > > > > and another > > > > > > head(rangeData2) > > > RangedData with 6 rows and 0 value columns across 25 spaces > > > space ranges | > > > <character> <iranges> | > > > 1 chr1 [ 90, 200] | > > > 2 chr1 [ 600, 650] | > > > 3 chr1 [ 306, 384] | > > > 4 chr2 [ 650, 690] | > > > 5 chr3 [ 315, 697] | > > > 6 chr5 [ 140, 228] | > > > > > > Would it be possible to merge these two so that I get something like > > this: > > > RangeData3 > > > RangedData with 7 rows and 0 value columns across 25 spaces > > > space ranges | > > > <character> <iranges> | > > > 1 chr1 [ 90, 283] | > > > 2 chr1 [ 600, 710] | > > > 3 chr1 [ 306, 450] | > > > 4 chr2 [ 582, 690] | > > > 5 chr3 [ 315, 697] | > > > 6 chr4 [ 40, 128] | > > > 7 chr5 [ 140, 228] | > > > > > > > > > Thanks for the help! > > > > > > Sincerely, > > > > > > Vishal > > > > > > [[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]] > > _______________________________________________ > 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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Thanks so much! It works great! -vishal On Fri, Nov 12, 2010 at 4:53 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > > > On Fri, Nov 12, 2010 at 12:18 PM, Vishal Thapar <vishalthapar@gmail.com>wrote: > >> Hi Kasper, >> >> Thank you for replying back. I had tried this earlier, but what I get is >> not >> what I expected. I sort of wanted to "merge" the ranges for each "chr" >> value. So I want to ranges in Chr1 to be merged separately from Chr2 and >> so >> on. What I Get is: >> >> > abc.chr=c("chr1","chr1","chr1","chr2","chr3","chr4") >> > abc.start=c(101,704,310,582,422,40) >> > abc.end = c(283,710,450,635,548,128) >> > >> > def.chr=c("chr1","chr1","chr1","chr2","chr3","chr5") >> > def.start=c(90,600,306,650,315,140) >> > def.end=c(200,650,384,690,697,228) >> > >> > I1 <- IRanges(start = abc.start, end = abc.end, names=abc.chr) >> > I2<- IRanges(start = def.start, end = def.end, names=def.chr) >> > >> > I1 >> IRanges of length 6 >> start end width names >> [1] 101 283 183 chr1 >> [2] 704 710 7 chr1 >> [3] 310 450 141 chr1 >> [4] 582 635 54 chr2 >> [5] 422 548 127 chr3 >> [6] 40 128 89 chr4 >> > I2 >> IRanges of length 6 >> start end width names >> [1] 90 200 111 chr1 >> [2] 600 650 51 chr1 >> [3] 306 384 79 chr1 >> [4] 650 690 41 chr2 >> [5] 315 697 383 chr3 >> [6] 140 228 89 chr5 >> > >> > xyz<- reduce(c(I1,I2)) >> > xyz >> IRanges of length 3 >> start end width >> [1] 40 283 244 >> [2] 306 697 392 >> [3] 704 710 7 >> >> >> What I would like is : >> xyz >> IRanges of length 7 >> start end width names >> [1] 90 283 194 chr1 >> [2] 600 710 111 chr1 >> [3] 306 450 145 chr1 >> [4] 582 690 108 chr2 >> [5] 315 697 383 chr3 >> [6] 40 128 89 chr4 >> [7] 140 228 89 chr5 >> >> >> This doesn't take the "names" into account while reducing / merging. Is >> there a way to have that taken into account while merging? >> >> > Yes, RangedData takes that into account. So you could do > > reduce(rbind(rangedData1, rangedData2)) > > To get out a RangedData of your merged ranges. > > Btw, Kasper's code works for GRanges but not IRanges. > > >> Thanks again for your help. >> >> -vishal >> >> On Fri, Nov 12, 2010 at 2:55 PM, Kasper Daniel Hansen < >> kasperdanielhansen@gmail.com> wrote: >> >> > ir1, ir2 are your IRanges >> > >> > do >> > reduce(c(ir1, ir2)) >> > >> > Kasper >> > >> > On Fri, Nov 12, 2010 at 2:49 PM, Vishal Thapar <vishalthapar@gmail.com> >> > wrote: >> > > Hi All, >> > > >> > > I have a question about how to merge / have a union of 2 RangeData >> > objects >> > > Say I have a rangeData1 >> > > head(rangeData1) >> > > RangedData with 6 rows and 0 value columns across 25 spaces >> > > space ranges | >> > > <character> <iranges> | >> > > 1 chr1 [ 101, 283] | >> > > 2 chr1 [ 704, 710] | >> > > 3 chr1 [ 310, 450] | >> > > 4 chr2 [ 582, 635] | >> > > 5 chr3 [ 422, 548] | >> > > 6 chr4 [ 40, 128] | >> > > >> > > and another >> > > >> > > head(rangeData2) >> > > RangedData with 6 rows and 0 value columns across 25 spaces >> > > space ranges | >> > > <character> <iranges> | >> > > 1 chr1 [ 90, 200] | >> > > 2 chr1 [ 600, 650] | >> > > 3 chr1 [ 306, 384] | >> > > 4 chr2 [ 650, 690] | >> > > 5 chr3 [ 315, 697] | >> > > 6 chr5 [ 140, 228] | >> > > >> > > Would it be possible to merge these two so that I get something like >> > this: >> > > RangeData3 >> > > RangedData with 7 rows and 0 value columns across 25 spaces >> > > space ranges | >> > > <character> <iranges> | >> > > 1 chr1 [ 90, 283] | >> > > 2 chr1 [ 600, 710] | >> > > 3 chr1 [ 306, 450] | >> > > 4 chr2 [ 582, 690] | >> > > 5 chr3 [ 315, 697] | >> > > 6 chr4 [ 40, 128] | >> > > 7 chr5 [ 140, 228] | >> > > >> > > >> > > Thanks for the help! >> > > >> > > Sincerely, >> > > >> > > Vishal >> > > >> > > [[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]] >> >> _______________________________________________ >> 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 >> > > -- *Vishal Thapar, Ph.D.* *Scientific informatics Analyst Cold Spring Harbor Lab Quick Bldg, Lowe Lab 1 Bungtown Road Cold Spring Harbor, NY - 11724* [[alternative HTML version deleted]]
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