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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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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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