On 03/21/2014 11:33 AM, Ou, Jianhong wrote:
Yes, I am calling reduce on a GRanges object. I just hate any warning or
error message. That's all.
I'm sympathetic: I hate them too :-)
So in GenomicRanges 1.15.40 (should become available tomorrow), you
should be able to use the new 'with.revmap' arg when reducing your
GRanges object. That will get rid of the warning.
Let me know if you run into any further issue with this.
Thanks,
H.
Yours Sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 3/21/14 1:26 PM, "Hervé Pagès" <hpa...@fhcrc.org> wrote:
Hi Jianhong,
On 03/21/2014 07:01 AM, Ou, Jianhong wrote:
Hi,
When I run sample code for reduce, I got Warning message:
The 'with.mapping' argument is deprecated.
Please use the 'with.revmap' argument instead.
Not really a bug, just a warning that the 'with.mapping' arg is being
replaced by the 'with.revmap' arg, except that 'with.revmap' is not
available yet when reducing a GRanges object... sorry :-/ Will be in
the next couple of days.
Note that it's already available when reducing an IRanges object,
but I suspect in your case you're calling reduce() on a GRanges object
right?
Thanks,
H.
Yours Sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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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...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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