[BioC] find differences between two sets of ranges

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Jul 4 19:50:28 CEST 2011

Hi Adreia,

On Mon, Jul 4, 2011 at 1:36 PM, Andreia Fonseca
<andreia.fonseca at gmail.com> wrote:
> Hi Martin,
> thanks for your email. Below you can find a head of each of the objects and
> the sessionInfo. Is this what you were asking?

Unlikely :-)

We would only need an example of a *small number* of ranges that shows
the problem that you have and allows us to play with it. So -- reduce
your CompressedRangesList into something that you can paste into an
email (using dput, for example) that we can then copy and play with.

For instance, `x` is a small IRangesList I have in my workspace. The
output of dput is:

R> dput(x)
    , elementType = "IRanges"
    , elementMetadata = NULL
    , metadata = list()
    , partitioning = new("PartitioningByEnd"
    , end = c(3L, 7L)
    , NAMES = NULL
    , elementType = "integer"
    , elementMetadata = NULL
    , metadata = list()
    , unlistData = new("IRanges"
    , start = c(1L, 2L, 3L, 15L, 45L, 20L, 1L)
    , width = c(5L, 1L, 6L, 1L, 56L, 61L, 5L)
    , NAMES = NULL
    , elementType = "integer"
    , elementMetadata = NULL
    , metadata = list()

If you now copy the result of that and assign it to a variable in your
workspace, eg:

R> my.yours <- new("CompressedIRangesList", ...)

You'l see that you now have the same IRangesList that I may be having
problems with ... so ... give us some objects like this that we can
then reconstruct and play with to see how to get you the answer you
want ...

Make sense?


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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