On 04/17/2015 10:00 AM, Michael Lawrence wrote:
Is that the case here? He has an Rle as an mcol in the GRanges, so in general expanding it will not align with the other components.
Not sure what you mean. Can you give an example? H.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> wrote: Hi, I think we should just expand the Rle internally. That will produce a numeric vector of the length of the GRanges i.e. it will be the same size as the start and end components of the GRanges object itself. No big deal at all. I'll make that change. H. On 04/17/2015 09:00 AM, Michael Lawrence wrote: Ideally it should be supported, but it would take some work as the coverage stuff is all in C. Could you give more details on your use case? For example, if you already have a range for every position on the chromosome, you could just extract the score column. I'm guessing it's more complicated than that. If the zeros are the problem, you could just subset the GRanges to remove the ranges with zero score, and then coerce the score to numeric before calling coverage. Michael 2015-04-17 8:00 GMT-07:00 Philip Lijnzaad <p.lijnz...@umcutrecht.nl <mailto:p.lijnz...@umcutrecht.nl>>: Dear all, I'm puzzled by the following behaviour: Given n <- 10 gr <- GRanges(seqnames=Rle('A', n), ranges=IRanges(1:n, width=1), score=Rle(5,n)) If I do coverage(gr,weight='score') I get Error in .normarg_shift_or_weight(weight, "weight", x) : 'weight' must be a numeric vector, a single string, or a list-like object Surely 'score' should be allowed to be an Rle? Especially given the fact that the return value of coverage(x,weight="score") when score is plain numeric vector is always an Rle ! Is this the expected behaviour? If so, I would argue that violates the principle of least suprise :-) The background to this is that I do numerical analysis on derived numerical data along my chromosomes. It contains many contiguous zeroes so it would be wasteful to cast everything down using as.numeric(). This is R version 3.01 on x86_64 Linux, Bioconductor version 2.13, package.version("IRanges") [1] "1.20.7" package.version("GenomicRanges") [1] "1.14.4" Regards, Philip -- Philip Lijnzaad, PhD Molecular Cancer Research University Medical Center (UMC), Utrecht Stratenum room 2.211 IM: plijnz...@jabber.org <mailto:plijnz...@jabber.org> , philip.lijnz...@gmail.com <mailto:philip.lijnz...@gmail.com> P.O. Box 85060, 3508 AB Utrecht (Universiteitsweg 100, 3584 CG Utrecht) The Netherlands tel: +31 (0)8875 68464 <tel:%2B31%20%280%298875%2068464> ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and ...{{dropped:10}} _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list 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...@fredhutch.org <mailto:hpa...@fredhutch.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...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
