Granges for chromosome interactions
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Bogdan ▴ 670
@bogdan-2367
Last seen 5 months ago
Palo Alto, CA, USA
Dear all, I would like to represent 2 (chromosomal) interactions as Granges data structure: let's say : chr1 1000-1010 site interacting with chr1 5000-5010 chr1 5000-5010 site interacting with chr1 8000-8010 in order to apply the function georm_arch in ggbio for visualization ... I would appreciate any suggestions in this respect. thanks very much, Bogdan [[alternative HTML version deleted]]
ggbio ggbio • 833 views
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 3.5 years ago
United States
Probably the smartest way to do this seems like the 'r3Cseq' package, which comes with an example. But it uses RangedData for now. R> biocLite(c('r3Cseq','BSgenome.Mmusculus.UCSC.mm9')) ## time passes R> require(r3Cseq) R> library(BSgenome.Mmusculus.UCSC.mm9) R> load(system.file("data","example.data.rda",package="r3Cseq")) R> calculateRPM(my.data) R> getInteractions(my.data) R> plotOverviewInteractions(my.data) Another, less smart, idea: add valuesinteractions.GR)$interactsWith as a SimpleList and walk through the list as needed? R> int.GR <- as(foo, 'GenomicRanges') R> showint.GR) ## GRanges with 6 ranges and 1 elementMetadata col: ## seqnames ranges strand | interactsWith ## <rle> <iranges> <rle> | <list> ## A1BG chr19 [ 63549984, 63565932] - | ######## ## NAT2 chr8 [ 18293035, 18303003] + | ######## ## ADA chr20 [ 42681577, 42713790] - | ######## ## CDH2 chr18 [ 23784933, 24011189] - | ######## ## AKT3 chr1 [241718158, 242073207] - | ######## ## LOC100009676 chr3 [102877980, 102880471] + | ######## ## ... R> valuesint.GR)$interactsWith <- SimpleList( c(2,3), c(1,4), c(), c(1), c(6), c(5) ) R> invisible(lapply( valuesint.GR)$interactsWith, function(x) cat(namesint.GR)[x], "\n" ))) ## NAT2 ADA ## A1BG CDH2 ## ## A1BG ## LOC100009676 ## AKT3 Per above, this would be the disrecommended approach, as far as I know. Hope this helps. --t On Tue, Aug 7, 2012 at 10:14 AM, Bogdan Tanasa <tanasa at="" gmail.com=""> wrote: > > Dear all, > > I would like to represent 2 (chromosomal) interactions as Granges data > structure: > > let's say : > chr1 1000-1010 site interacting with chr1 5000-5010 > chr1 5000-5010 site interacting with chr1 8000-8010 > > in order to apply the function georm_arch in ggbio for visualization ... > > I would appreciate any suggestions in this respect. thanks very much, > > Bogdan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- A model is a lie that helps you see the truth. Howard Skipper
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