[Bioc-devel] New argument 'use.names' in granges() function

[Leonard Goldstein]

Thanks Hervé.

Leonard

On Fri, Jun 17, 2016 at 2:11 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Done in SGSeq 1.6.3 (release) and 1.7.4 (devel).
>
> Also done in SomaticSignatures 2.8.4 (release) and 2.9.4 (devel).
>
> I scanned the entire Rpacks folder and those are the only 2 packages
> I found that contain calls to granges() with 2 unnamed arguments.
>
> Sorry for the trouble.
>
> H.
>
>
> On 06/16/2016 11:55 PM, Hervé Pagès wrote:
>
>> Hi Leonard,
>>
>> I really like having 'use.names' before 'use.mcols'. Sorry for breaking
>> SGSeq, I'll fix it.
>>
>> FWIW I think it's good practice to always name this kind of arguments.
>> Not the first argument 'x' or the first 2 arguments 'x' and 'y' of a
>> unary or binary function, but the toggles that follow them like
>> 'use.names', 'use.mcols', 'ignore.strand' etc..
>> That makes the code a lot more readable.
>>
>> Cheers,
>> H.
>>
>>
>> On 06/16/2016 04:46 PM, Leonard Goldstein wrote:
>>
>>> Hi Hervé,
>>>
>>> I noticed a recent change in the release and development version of
>>> GenomicRanges, which introduces a new argument 'use.names' for granges()
>>> and other functions.
>>>
>>> The change breaks the SGSeq package, since it uses granges() relying on
>>> positional argument matching (and 'use.names' has been added preceding
>>> existing arguments). Should GenomicRanges be changed so that newly
>>> arguments occur after existing arguments? Otherwise I can fix the problem
>>> in SGSeq.
>>>
>>> Many thanks,
>>>
>>> Leonard
>>>
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>>>
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>>> Bioc-devel at r-project.org mailing list
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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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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