Sorry, I was confused. You're right, there's not much point in keeping it compressed.
On Fri, Apr 17, 2015 at 10:14 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
