On Thu, Apr 17, 2014 at 11:00 AM, Michael Lawrence <
lawrence.michael@gene.com> wrote:

> Ok, I had assumed that even disabling that feature would generate a
> GRangesList.
>
>
> On Thu, Apr 17, 2014 at 10:51 AM, Hervé Pagès <hpages@fhcrc.org> wrote:
>
>> Hi Vince, Michael,
>>
>>
>> On 04/17/2014 10:40 AM, Michael Lawrence wrote:
>>
>>> On Thu, Apr 17, 2014 at 10:27 AM, Vince S. Buffalo <vsbuffalo@gmail.com
>>> >wrote:
>>>
>>>  Sorry to return to this older topic, but I'm curious -- what's the
>>>>
>>>> reasoning behind allocating tiles of 1L then using resize?
>>>>
>>>> tiles <- unlist(tileGenome(seqinfo(snps), tilewidth=1L))
>>>> windows <- resize(tiles, 500L) # you will get a warning about trimming
>>>>
>>>>
>>>>  This is the way to generate sliding windows. The tileGenome generates a
>>> partitioning, i.e., non-overlapping windows.
>>>
>>
Oh, *very* clever!


>
>>>
>>>  Also, in general, why does tileGenome always return a list rather than a
>>>> GenomicRanges object?
>>>>
>>>>
>>>>  tileGenome can potentially generate multiple GRanges elements per tile,
>>> because by default tiles will cross between chromosomes in an effort to
>>> achieve constant tile width. Even when that feature is disabled, the
>>> result
>>> is still a GRangesList for consistency.
>>>
>>
>> To disable that feature, use 'cut.last.tile.in.chrom=TRUE'. Then it
>> returns a GRanges. See ?tileGenome
>>
>
Right, this makes sense too.

Thanks Hervé and Michael!

-- 
Vince Buffalo
Ross-Ibarra Lab (www.rilab.org)
Plant Sciences, UC Davis

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