I guess it would be helpful if you paste some code that reproduces your error. unique() should work the same on IRanges, whether you're running R 2.9 or 2.11 or 2.13, and in-between.
Thanks, Michael On Wed, Nov 3, 2010 at 10:48 AM, Kunbin Qu <[email protected]> wrote: > 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:[email protected]] > *Sent:* Wednesday, November 03, 2010 10:36 AM > *To:* Kunbin Qu > *Cc:* Steve Lianoglou; [email protected] > > *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 <[email protected]> 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:[email protected]] > Sent: Wednesday, November 03, 2010 9:38 AM > To: Kunbin Qu > Cc: [email protected] > 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 <[email protected]> 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> > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. 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