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

Hervé Pagès hpages at fredhutch.org
Fri Jun 17 08:55:40 CEST 2016

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.


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
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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