[Bioc-devel] as.character method for GenomicRanges?
Michael Lawrence
lawrence.michael at gene.com
Tue Sep 15 18:59:23 CEST 2015
Did this as.character method ever get added? It was a good idea, and we
should add it even though we haven't figured out the table stuff yet. It's
fine if it appends the strand whenever there is at least one range with +/-.
Michael
On Mon, Apr 27, 2015 at 2:23 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> On 04/27/2015 02:15 PM, Michael Lawrence wrote:
>
>> It would be nice to have a single function call that would hide these
>> details. It could probably be made more efficient also by avoiding
>> multiple matching, unnecessary revmap lists, etc. tableAsGRanges() is
>> not a good name but it conveys what I mean (does that make it actually
>> good?).
>>
>
> There is nothing specific to GRanges here. We're just reporting the
> frequency of unique elements in a metadata column so this belongs to
> the "extended" Vector API in the same way that findMatches/countMatches
> do.
>
> H.
>
>
>> On Mon, Apr 27, 2015 at 12:23 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> On 04/24/2015 11:41 AM, Michael Lawrence wrote:
>>
>> Taking this a bit off topic but it would be nice if we could get
>> the
>> GRanges equivalent of as.data.frame(table(x)), i.e., unique(x)
>> with a
>> count mcol. Should be easy to support but what should the API be
>> like?
>>
>>
>> This was actually the motivating use case for introducing
>> findMatches/countMatches a couple of years ago:
>>
>> ux <- unique(x)
>> mcols(ux)$Freq <- countMatches(ux, x)
>>
>> Don't know what a good API would be to make this even more
>> straightforward though. Maybe via some extra argument to unique()
>> e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
>> argument of reduce(). Note that unique() could also support the
>> 'with.revmap' arg. Once it does, the 'with.freq' arg can also
>> be implemented by just calling elementLengths() on the "revmap"
>> metadata column.
>>
>> H.
>>
>>
>> On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès
>> <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>>
>> wrote:
>>
>> On 04/24/2015 10:18 AM, Michael Lawrence 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.
>>
>>
>> It does use the 4-way int hash internally. as.character()
>> is only used
>> at the very-end to stick the names on the returned table
>> object.
>>
>> H.
>>
>>
>>
>> On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès
>> <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
>> <mailto:hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org> <mailto: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>
>> <mailto:phaverty at gene.com <mailto:phaverty at gene.com>>
>> <mailto:phaverty at gene.com <mailto:phaverty at gene.com>
>> <mailto:phaverty at gene.com <mailto:phaverty at gene.com>>>
>>
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>>
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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
>>
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>> <mailto:hpages at fredhutch.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>
>> <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>> <tel:%28206%29%20667-1319>
>>
>>
>>
>> --
>> 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>
>>
>>
>>
> --
> 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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