Added in IRanges 1.21.41. H.
On 04/01/2014 06:15 PM, Michael Lawrence wrote:
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 <mailto: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> <mailto: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-bounces@r-__project.org <mailto:bioc-devel-boun...@r-project.org>> [mailto:bioc-devel-bounces@r-____project.org <mailto:bioc-devel-bounces@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> <mailto: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> <mailto: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> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> ___________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> <mailto: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> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> ___________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> <mailto: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> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> -- 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> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> <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 <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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
