[Bioc-devel] Subsetting Lists by Lists

[Hervé Pagès]

On 04/01/2014 10:17 AM, Ryan wrote:
> That won't work if any vector has fewer than 5 elements. Maybe
>
> lapply(x, head, n=5)
>
> would work?

Yes. Note that you can use endoapply() to preserve the class of the
original object:

   > endoapply(cvg, head, n=5)
   RleList of length 3
   $chr1
   integer-Rle of length 5 with 2 runs
     Lengths: 4 1
     Values : 1 2

   $chr2
   integer-Rle of length 5 with 4 runs
     Lengths: 1 1 1 2
     Values : 0 1 2 3

   $chr3
   integer-Rle of length 5 with 1 run
     Lengths: 5
     Values : 0

But lapply- or endoapply-based solutions are slower than a [ based
solution. Unfortunately the latter requires too much munging to get
the subscript right:

   ## parallel seq_len()
   pseq_len <- function(eltlens)
   {
     ans_skeleton <- PartitioningByWidth(eltlens)
     tmp <- relist(seq_len(sum(eltlens)), ans_skeleton)
     tmp - start(ans_skeleton) + 1L
   }

Then:

   > pseq_len(c(5, 1, 0, 2))
   IntegerList of length 4
   [[1]] 1 2 3 4 5
   [[2]] 1
   [[3]] integer(0)
   [[4]] 1 2

   > cvg[pseq_len(pmin(elementLengths(cvg), 5))]
   RleList of length 3
   $chr1
   integer-Rle of length 5 with 2 runs
     Lengths: 4 1
     Values : 1 2

   $chr2
   integer-Rle of length 5 with 4 runs
     Lengths: 1 1 1 2
     Values : 0 1 2 3

   $chr3
   integer-Rle of length 5 with 1 run
     Lengths: 5
     Values : 0

H.

>
> On Tue Apr  1 09:24:51 2014, Cook, Malcolm wrote:
>> in the mean time,
>>
>> lapply(`[`,x,IntegerList(1:5))
>>
>> ??
>>
>>   >-----Original Message-----
>>   >From: bioc-devel-bounces at r-project.org
>> [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Michael Lawrence
>>   >Sent: Tuesday, April 01, 2014 9:21 AM
>>   >To: bioc-devel at r-project.org
>>   >Subject: [Bioc-devel] Subsetting Lists by Lists
>>   >
>>   >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]]
>>   >
>>   >_______________________________________________
>>   >Bioc-devel at r-project.org mailing list
>>   >https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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