[Bioc-devel] as.character method for GenomicRanges?

[Hervé Pagès]

On 04/24/2015 10:21 AM, Michael Lawrence wrote:
> Sorry, one more concern, if you're thinking of using as a range key, you
> will need the strand, but many use cases might not want the strand on
> there. Like for pasting into a genome browser.

What about appending the strand only for GRanges objects that
have at least one range that is not on *?

setMethod("as.character", "GenomicRanges",
     function(x)
     {
         if (length(x) == 0L)
             return(character(0))
         ans <- paste0(seqnames(x), ":", start(x), "-", end(x))
         if (any(strand(x) != "*"))
               ans <- paste0(ans, ":", strand(x))
         ans
     }
)

 > as.character(gr)
  [1] "chr1:1-10"  "chr2:2-10"  "chr2:3-10"  "chr2:4-10"  "chr1:5-10"
  [6] "chr1:6-10"  "chr3:7-10"  "chr3:8-10"  "chr3:9-10"  "chr3:10-10"

 > strand(gr)[2:3] <- c("-", "+")
 > as.character(gr)
  [1] "chr1:1-10:*"  "chr2:2-10:-"  "chr2:3-10:+"  "chr2:4-10:*" 
"chr1:5-10:*"
  [6] "chr1:6-10:*"  "chr3:7-10:*"  "chr3:8-10:*"  "chr3:9-10:*" 
"chr3:10-10:*"

H.

>
> On Fri, Apr 24, 2015 at 10:18 AM, Michael Lawrence <michafla at gene.com
> <mailto:michafla at gene.com>> wrote:
>
>     It is a great idea, but I'm not sure I would use it to implement
>     table(). Allocating those strings will be costly. Don't we already
>     have the 4-way int hash? Of course, my intuition might be completely
>     off here.
>
>
>     On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès <hpages at fredhutch.org
>     <mailto:hpages at fredhutch.org>> wrote:
>
>         Hi Pete,
>
>         Excellent idea. That will make things like table() work
>         out-of-the-box
>         on GenomicRanges objects. I'll add that.
>
>         Thanks,
>         H.
>
>
>
>         On 04/24/2015 09:43 AM, Peter Haverty wrote:
>
>             Would people be interested in having this:
>
>             setMethod("as.character", "GenomicRanges",
>                         function(x) {
>                             paste0(seqnames(x), ":", start(x), "-", end(x))
>                         })
>
>             ?
>
>             I find myself doing that a lot to make unique names or for
>             output that
>             goes to collaborators.  I suppose we might want to tack on
>             the strand if it
>             isn't "*".  I have some code for going the other direction
>             too, if there is
>             interest.
>
>
>
>             Pete
>
>             ____________________
>             Peter M. Haverty, Ph.D.
>             Genentech, Inc.
>             phaverty at gene.com <mailto:phaverty at gene.com>
>
>                      [[alternative HTML version deleted]]
>
>             _______________________________________________
>             Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>             mailing list
>             https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>         --
>         Hervé Pagès
>
>         Program in Computational Biology
>         Division of Public Health Sciences
>         Fred Hutchinson Cancer Research Center
>         1100 Fairview Ave. N, M1-B514
>         P.O. Box 19024
>         Seattle, WA 98109-1024
>
>         E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>         Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>         Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>
>         _______________________________________________
>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>         mailing list
>         https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319