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

[Peter Haverty]

Good catch. We'll want the strand in case we need to go back to a GRanges.
I would make the strand addition optional with the default of FALSE. It's
nice to have a column of strings you can paste right into a genome browser
(sorry Michael :-) ).  I often pass my bench collaborators a spreadsheet
with such a column.

Pete

____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com

On Fri, Apr 24, 2015 at 10:50 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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>
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>>
>>
>>         --
>>         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
>

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