[Bioc-devel] Subsetting Lists by Lists

Thanks Herve. I might not be so bad to have rep out in the unnamed case
(think of NULL names meaning wildcard). If we had:

i <- IntegerList(1:5)
x[i]

The 'i' does not really identify any one element in 'x'. If both 'i' and
'x' had names, then there would be a matching, but otherwise, truncating
'x' to length(i) is surprising, and it's hard to imagine a use-case for
it. In some ways, this is analogous to logical indexing, which is recycled.

But that said, my use case is really more of a pluckHead/Tail. Don't
worry about this release.

Michael



On Tue, Apr 1, 2014 at 12:06 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    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>
            [mailto: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

            <mailto: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]]
               >
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