[Bioc-devel] Subsetting Lists by Lists

[Hervé Pagès]

Hi Tim,

There is probably too much guess work for me to really be able to
help... However, and FWIW, in Bioc-devel the 'asRle' argument of
import() has been replaced by the 'as' argument and it can be set
to "GRanges", "RleList", or "NumericList". Be aware that, surprisingly,
if you specify a 'selection', then using as="RleList" vs
as="NumericList" not only changes the returned type but also the 
semantic of the function: the returned List object has 1 list element
per chromosome for the former and 1 list element per range in
'selection' for the latter.

(IMO it would probably be less confusing and less error-prone if
switching between these 2 semantics was decoupled from choosing
the returned type.)

Anyway, in your case maybe you want to use as="RleList".

Then for averaging the score over each of the range in your initial
'selection", maybe you'll find the examples section of the tileGenome()
function helpful (this is in the GenomicRanges package).

Am I on the right track with this?

Cheers,
H.

On 04/01/2014 10:40 AM, Tim Triche, Jr. wrote:
> Hi all,
>
> The following is tangentially related, but hopefully the answer will be useful to others (both directly and via my package, which prompts this)...
>
> Suppose I do this:
>
> dat <- GRangesList(
> lapply( bigWigFileNames, import,
>              selection=someRanges ) )
>
> Now I have a GRangesList of values, some of which have 0 ranges, some of which may have hundreds or thousands. I would like to aggregate and smooth over various subgroups of these for Gviz/trackViewer plots, so I was thinking of getting an RleList or similar out of the mcols() from each of the GRangesList atoms.
>
> However,
>
> 1) What is the "right" (fast, idiomatic, future-safe) way to extract and combine these ranges into columns of Rles might be.  I found something not-dissimilar in SpliceGraphs (or was it spliceGrapher?) but I imagine this is a common operation with some efficient "one true way" to do it.
>
> 2) should I be sucking these into a genoset or SummarizedExperiment instead?  I'll take the hit if I have to, once, but I don't want it to eat up all available RAM since I eventually wish to make the plotting process at least somewhat interactive (even if that means calling IGV or interactiveDisplay to do it).
>
> Thanks for any guidance you may have to offer,
>
> --t
>
>> On Apr 1, 2014, at 7:21 AM, Michael Lawrence <lawrence.michael at gene.com> wrote:
>>
>> Mostly to Herve:
>>
>> Sometimes we want to pluck the first 1, or 10, or whatever elements from
>> each element of a list. If I had a list 'x', I thought I could do this with:
>>
>> x[IntegerList(1:5)]
>>
>> But it only gives elements 1:5 from x[[1]], not each element of 'x'. In
>> other words, I thought the index would be repped out. Instead, 'x' is
>> subset to the length of 'i', and I'm not sure if that makes sense?
>>
>> But maybe what we really want are pluckHead/Tail, which would be robust to
>> the case that < n elements are in an element. And of course a more general
>> pluck(x, i) to select 'i' from each element, but I wanted the line above to
>> do that.
>>
>> Michael
>>
>>     [[alternative HTML version deleted]]
>>
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>
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-- 
Hervé Pagès

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