Yes, I do have that. Does this mean that whenever I need to use "unique" from IRanges, I need to use "selectMethod" to notify R which "unique" I am using, and include the object I am targeting in the "selectMethod" call? Thanks.



From: Michael Lawrence [mailto:lawrence.michael@gene.com]
Sent: Wednesday, November 03, 2010 10:36 AM
To: Kunbin Qu
Cc: Steve Lianoglou; Bioc-sig-sequencing@r-project.org
Subject: Re: [Bioc-sig-seq] how to access the "unique" function in IRanges

So when you type:

selectMethod(unique, class(IRanges(start=c(20L, 8L, 20L, 22L), width=c(5L, 3L, 5L, 2L))))

In your R 2.11 version, do you get this result?

Method Definition:

function (x, incomparables = FALSE, ...)
{
    .local <- function (x, incomparables = FALSE, fromLast = FALSE,
        method = c("quick", "hash"), ...)
    {
        x[!duplicated(x, incomparables = incomparables, fromLast = fromLast,
            method = method, ...)]
    }
    .local(x, incomparables, ...)
}
<environment: namespace:IRanges>

Signatures:
        x
target  "Ranges"
defined "Ranges"
On Wed, Nov 3, 2010 at 10:25 AM, Kunbin Qu <KQu@genomichealth.com<mailto:KQu@genomichealth.com>> wrote:
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)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

Hi,

On Wed, Nov 3, 2010 at 12:12 PM, Kunbin Qu <KQu@genomichealth.com<mailto:KQu@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

--
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<http://cbio.mskcc.org/%7Elianos/contact>
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