I like phead/ptail. I was going to write them, so thanks for taking care of
it!
Michael
On Tue, Apr 1, 2014 at 3:24 PM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> On 04/01/2014 02:43 PM, Michael Lawrence wrote:
>
>> 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.
>>
>
> The pseq_len() utility I sent previously solves your pluckHead()
> problem:
>
> pluckHead <- function(x, n=6)
> {
> x[pseq_len(pmin(elementLengths(x), n))]
> }
>
> or, using the non-exported utility IRanges:::fancy_mseq():
>
> pluckHead <- function(x, n=6)
> {
> x_eltlens <- unname(elementLengths(x))
> i_eltlens <- pmin(x_eltlens, n)
> i_skeleton <- PartitioningByEnd(cumsum(i_eltlens), names=names(x))
> unlisted_i <- IRanges:::fancy_mseq(i_eltlens)
> i <- relist(unlisted_i, i_skeleton)
> x[i]
> }
>
> For pluckTail():
>
> pluckTail <- function(x, n=6)
> {
> x_eltlens <- unname(elementLengths(x))
> i_eltlens <- pmin(x_eltlens, n)
> i_skeleton <- PartitioningByEnd(cumsum(i_eltlens), names=names(x))
> offset <- x_eltlens - i_eltlens
> unlisted_i <- IRanges:::fancy_mseq(i_eltlens, offset)
> i <- relist(unlisted_i, i_skeleton)
> x[i]
> }
>
> For both, 'n' can be of length > 1 and is recycled to the length of 'x'.
> Negative values in 'n' are not supported but that should be easy to
> add.
>
> So I could add these 2 functions to IRanges, however, I'm not totally
> convinced by the names. What about phead() and ptail() ("p" for
> "parallel"), or vhead() and vtail() ("v" for "vectorized"), or mhead()
> and mtail() (they're just fast equivalent to 'mapply(head, x, n)' and
> 'mapply(tail, x, n))', or...?
>
> Thanks,
> H.
>
>
>> Michael
>>
>>
>>
>> On Tue, Apr 1, 2014 at 12:06 PM, Hervé Pagès <hpa...@fhcrc.org
>> <mailto:hpa...@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@r-project.__org
>> <mailto:bioc-devel-boun...@r-project.org>
>> [mailto:bioc-devel-bounces@r-__project.org
>> <mailto:bioc-devel-boun...@r-project.org>] On Behalf Of
>> Michael Lawrence
>> >Sent: Tuesday, April 01, 2014 9:21 AM
>> >To: bioc-devel@r-project.org
>> <mailto:bioc-devel@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@r-project.org
>> <mailto:Bioc-devel@r-project.org> mailing list
>> >https://stat.ethz.ch/mailman/__listinfo/bioc-devel
>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>
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>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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