[Bioc-sig-seq] how to access the "unique" function in IRanges

Kunbin Qu KQu at genomichealth.com
Wed Nov 3 18:25:27 CET 2010

Steve, here is a simple example on what I'd like to do: I want to eliminate the duplicated IRanges from the IRanges list. R-2.9.2 seems to have the "unique" function visible to the end user, but not the R-2.11.0 version which has all our current installation:

> x <- IRanges(start=c(20L, 8L, 20L, 22L), width=c(5L, 3L, 5L, 2L))
> x
IRanges object:
    start end width
[1]    20  24     5
[2]     8  10     3
[3]    20  24     5
[4]    22  23     2
> unique(x)
IRanges object:
    start end width
[1]    20  24     5
[2]     8  10     3
[3]    22  23     2
> sessionInfo()
R version 2.9.2 (2009-08-24) 


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ShortRead_1.2.1    lattice_0.17-26    BSgenome_1.12.5    Biostrings_2.12.10
[5] IRanges_1.2.3     

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 grid_2.9.2    hwriter_1.2   tools_2.9.2  

-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: Wednesday, November 03, 2010 9:38 AM
To: Kunbin Qu
Cc: Bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] how to access the "unique" function in IRanges


On Wed, Nov 3, 2010 at 12:12 PM, Kunbin Qu <KQu at genomichealth.com> wrote:
> Dear All,
> I have a RangedDataList which has many duplicated IRanges. I would like to have a unique set from the original IRanges. I was trying to use the "unique" function, by IRanges::unique (see below), but somehow it was still called from the base. Is there a way to access the unique function, or some other functions I can use to get a unique set of the original IRanges? Thanks.

Can you give a small example of the data that you, and also the result
you expect so we can try to work with it? Maybe you can dput() the
first few elements of your list, or just give a simple toy example in
another way that we could paste into an R session easily.

I'm not sure what you want your end result to be -- do you want to
remove elements in your RangedDataList that contain IRanges that
appear in other parts of the list? Also, why aren't you using an
IRangesList if you are storing IRanges in a list(?))


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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