Thank you all. On Thu, Sep 6, 2012 at 11:33 PM, Martin Morgan wrote: > On 09/06/2012 11:33 AM, d r wrote: > >> Thank you Mike and Valarie, >> >> Just to be sure I understood you clearly: I understand there is no >> possibilty to use subdivideGRanges() to split a GRanges to a given number >> of elements. >> If I understood you correctly, it is also not possible to read a vector >> into the subsize argument. is taht true or is ther some possibilty to do >> that? >> > > > Not sure if this is the best way, but for a GRanges instance 'gr' dividing > it in to 'n' bins, you might start by making sure there won't be any > zero-width or necessarily overlapping bins > > > if (any(width(gr) < n)) > stop("all 'width(gr)' must be >= 'n'") > > then figure out the width, in numeric values, of each bin > > d <- width(gr) / n > > To make a vector of offsets from the start of each original bin, you want > to do this in a 'vectorized' fashion, rather than a loop, so I replicated > each element of d n times, calculated the cumulative sum, and then > subtracted for each of the d x n elements the value of the cumulative sum > at the start of each replicate, a little obscure I guess... > > dd <- cumsum(rep(d, each=n)) > mask <- logical(n); mask[1] <- TRUE # every n'th is base for range > dd <- dd - rep(dd[mask], each=n) > > To get the new starts, replicate the original starts and add the offsets, > using round() to approximate to the nearest integer value > > starts <- round(rep(start(gr), each=n) + dd) > > the ends will be the starts of the next range, minus 1 (the 'L' says to > represent 0 and 1 as integer values, rather than numeric, and avoids > unnecessary coercion from integer to numeric and back) > > ends <- c(starts[-1] - 1L, 0L) > > except for each of the n'th (including last) elements, which will be the > end of the original range > > ends[rev(mask)] <- end(gr) > > we can then replicate our original data and update the ranges > > gr <- gr[rep(seq_along(gr), each=n)] > ranges(gr) <- IRanges(starts, ends) > > getting the result > > gr > > Here's the above as a function > > intoNbins <- > function(gr, n = 10) > { > if (any(width(gr) < n)) > stop("all 'width(gr)' must be >= 'n'") > d <- width(gr) / n > dd <- cumsum(rep(d, each=n)) > mask <- logical(n); mask[1] <- TRUE > dd <- dd - rep(dd[mask], each=n) > > starts <- round(rep(start(gr), each=n) + dd) > ends <- c(starts[-1], 0) - 1L > ends[rev(mask)] <- end(gr) > > gr <- gr[rep(seq_along(gr), each=n)] > ranges(gr) <- IRanges(starts, ends) > gr > } > > and in action > > > gr <- GRanges("A", IRanges(c(1, 21, 21), width=c(10, 20, 30))) > > table(width(intoNbins(gr, 10))) > > 1 2 3 > 10 10 10 > > It might make sense to split the GRanges into a GRangesList, one element > for each CpG island, replacing the last line of intoNbins with > > split(gr, rep(seq_along(d), each=n)) > > Martin > > >> thanks again >> Dolev >> >> On Thu, Sep 6, 2012 at 5:17 PM, Michael Love wrote: >> >> Hi Dolev, >>> >>> The subdivideGRanges() function cannot accomplish this task. >>> >>> from the manual: >>> >>> "Takes an input GRanges object and, splits each range into multiple >>> ranges >>> of nearly equal width. For an input range of width w and subdividing size >>> s, it will subdivide the range into max(1,floor(w/s)) nearly equal width >>> ranges." >>> >>> So the function tries to keep the widths of the subdivided ranges around >>> s >>> basepairs, rather than keeping the number of subdivided ranges constant. >>> >>> I will include a more helpful error message if a vector is provided for >>> the subsize argument. >>> >>> cheers, >>> >>> Mike >>> >>> >>> >>> On 09/06/12 16:02, Valerie Obenchain wrote: >>> >>> Hi Dolev, >>>> >>>> I am copying the maintainer of exomeCopy which is the package >>>> subdivideGRanges() comes from. Please provide a small reproducable >>>> example >>>> of the problem you are having (i.e., a few lines of code that someone >>>> else >>>> can run to get the same error). This makes it easier for others to help. >>>> >>>> Valerie >>>> >>>> On 09/06/12 04:39, d r wrote: >>>> >>>> Hello >>>>> >>>>> I have a GRanges object representing CpG islands, that I want to >>>>> subdivide >>>>> so that each island will be represented by 10 ranges of equal width. >>>>> >>>>> To do this, I created a vector containing the widths of the islands >>>>> divided >>>>> by ten: >>>>> >>>>> swidth<-as.integer(width(****islandshg19)/10) >>>>> >>>>> >>>>> >>>>> and then called subdivideGRanges(): >>>>> >>>>> >>>>> islandshg19<-subdivideGRanges(****islandshg19, >>>>> >>>>> subsize=as.integer(width/10)) >>>>> >>>>> >>>>> and got a multitude of warnings. >>>>> >>>>> >>>>> This approach did work when I tried it on a GRanges object containing a >>>>> single range, and a width vector of length 1. When I tried to extend >>>>> the >>>>> sample to include two objetcs, I got these warning message: >>>>> >>>>> 1: In if (widths[i]< 2 * subsize) { ... : >>>>> >>>>> the condition has length> 1 and only the first element will be >>>>> used >>>>> >>>>> 2: In if (width< 2 * subsize) { ... : >>>>> >>>>> the condition has length> 1 and only the first element will be >>>>> used >>>>> >>>>> 3: In 0:(nchunks - 1) : numerical expression has 2 elements: only the >>>>> first used >>>>> >>>>> >>>>> >>>>> Which makes me think that the problem may be related to assigning the >>>>> right >>>>> subszie to the the rigth range. >>>>> >>>>> Does anyone have an idea how to do that? >>>>> >>>>> Thanks in advance >>>>> >>>>> Dolev Rahat >>>>> >>>>> >>>>> >>>>> sessionInfo(if required): >>>>> >>>>> R version 2.15.1 (2012-06-22) >>>>> >>>>> Platform: x86_64-pc-mingw32/x64 (64-bit) >>>>> >>>>> >>>>> >>>>> locale: >>>>> >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>> >>>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>>> States.1252 >>>>> >>>>> >>>>> >>>>> attached base packages: >>>>> >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> >>>>> >>>>> other attached packages: >>>>> >>>>> [1] exomeCopy_1.2.0 Rsamtools_1.8.6 Biostrings_2.24.1 >>>>> rtracklayer_1.16.3 taRifx_1.0.4 reshape2_1.2.1 >>>>> plyr_1.7.1 >>>>> >>>>> [8] XML_3.9-4.1 GenomicRanges_1.9.54 IRanges_1.15.40 >>>>> BiocGenerics_0.3.1 BiocInstaller_1.4.7 >>>>> >>>>> >>>>> >>>>> loaded via a namespace (and not attached): >>>>> >>>>> [1] bitops_1.0-4.1 BSgenome_1.25.7 RCurl_1.91-1.1 stats4_2.15.1 >>>>> stringr_0.6.1 tools_2.15.1 zlibbioc_1.2.0 >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________****_________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/****listinfo/bioconductor >>>>> >>>>> > >>>>> Search the archives: http://news.gmane.org/gmane.** >>>>> science.biology.informatics.****conductor>>>> org/gmane.science.biology.**informatics.conductor >>>>> > >>>>> >>>>> >>>> >>>> >>> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]