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' a
Some of the inconsistency emerges from wrappers that correspond to
operations on the rowData. I think that's fine as long as it's obvious (as
in the case of findOverlaps and isSNV). The head and tail functions are by
convention row-based for rectangular objects. I agree though that if we
keep 1D e
Hi Martin,
On 03/21/2014 01:45 PM, Martin Morgan wrote:
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little
surprising;
I learned it from restrictToSNV.
This is inherited from Summariz
1D extraction on matrices (treating them as a 1D vector) is actually
useful, but I don't see how that would really make sense here. This is an
inconsistency, and inconsistencies are often OK when there is a benefit
(like gr$foo), but unless I'm missing something the benefit here seems to
be x[i] vs
hi Valerie,
Thanks. I'm trying now to make use of the new mate pairing algorithm but
keeping running out of memory (i requested 50 Gb) and getting my job
killed. I wonder if you could try this code/example below?
If the new C code is faster for paired-end than the pre-sorting/obeyQname
method tha
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
This is inherited from SummarizedExperiment:
> example(SummarizedExperiment)
> se
Yes, I am calling reduce on a GRanges object. I just hate any warning or
error message. That's all.
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" wrote:
>Hi Jianhong,
>
>On 03/21/201
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
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.
Yours Sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
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