[BioC] Granges for chromosome interactions

[Tim Triche, Jr.]

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 values(interactions.GR)$interactsWith
as a SimpleList and walk through the list as needed?

R> int.GR <- as(foo, 'GenomicRanges')
R> show(int.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> values(int.GR)$interactsWith <- SimpleList( c(2,3), c(1,4), c(),
c(1), c(6), c(5) )
R> invisible(lapply( values(int.GR)$interactsWith, function(x)
cat(names(int.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]]
>
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