On 02/22/2014 01:59 PM, Michael Lawrence wrote:
> Yea, I can see the argument for consistency. Not sure I'll get around to
> it though. How about we see if they take this patch first.
Sounds good. I was hoping that fixing selectMethod would maybe
fix ?generic(arg) automatically but that's probably too naive.
In the meantime I tried the patch and got:
> library(IRanges)
> ?coverage(IRanges())
Error in args$...[[1L]] : object of type 'symbol' is not subsettable
> library(rtracklayer)
> path_to_gff <- system.file("tests", "v1.gff", package = "rtracklayer")
> ?import(path_to_gff)
Error in args$...[[1L]] : object of type 'symbol' is not subsettable
which seems to go away if I add the following line
args <- args[fdef at signature]
right before
args$... <- args$...[[1L]]
like you did in your original helpwith() proposal.
Also I found a situation that is still failing (with or without the
patch):
> ?c(IRanges(),IRanges())
Error in .helpForCall(topicExpr, parent.frame()) :
no documentation for function ‘c’ and signature ‘x = "IRanges",
recursive = "logical"’
In addition: Warning message:
In .helpForCall(topicExpr, parent.frame()) :
no method defined for function ‘c’ and signature ‘x = "IRanges",
recursive = "logical"’
Thanks again for working on this.
H.
>
> Michael
>
>
> On Sat, Feb 22, 2014 at 12:26 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> wrote:
>
> Thanks Michael.
>
> Do you think it would be sensible to offer a similar fix for
> selectMethod?
>
> > setGeneric("f", function(x, y) standardGeneric("f"))
> > setMethod("f", c("numeric", "missing"), function(x, y) x)
> > selectMethod("f", "numeric")
> Error in selectMethod("f", "numeric") :
> no method found for signature numeric, ANY
>
> In a perfect world,
>
> generic(arg)
> selectMethod(generic, class(arg))
> ?generic(arg)
>
> should behave consistently.
>
> The ?import(path_to_gff) error I reported earlier was actually
> inspired by a sad experience I had in the past where I was trying
> to use selectMethod("import", ...) to find out what particular
> method was being called (I needed to see the code).
>
> Thanks,
> H.
>
>
> On 02/22/2014 05:59 AM, Michael Lawrence wrote:
>
> Translated it into a patch against R, submitted here:
> https://bugs.r-project.org/__bugzilla3/show_bug.cgi?id=__15680
> <https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15680>
>
>
> On Fri, Feb 21, 2014 at 2:53 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>> wrote:
>
>
>
> On 02/21/2014 02:01 PM, Michael Lawrence wrote:
>
> This function seems to solve the problem:
>
> helpwith <- function(expr) {
> env <- IRanges:::top_prenv(expr)
> expr <- substitute(expr)
> fun <- eval(expr[[1L]], env)
> fun.name <http://fun.name> <http://fun.name> <http://fun.name>
> <- deparse(expr[[1L]])
> if (!isGeneric(fun.name <http://fun.name>
> <http://fun.name> <http://fun.name>,
> env)) {
>
> stop("'expr' must be a call to a generic")
> }
> args <- formals(fun)
> mc <- match.call(fun, expr, expand.dots=FALSE)
> args[names(mc[-1L])] <- mc[-1L]
> args <- args[fun at signature]
> args$... <- args$...[[1L]]
> target.sig <- vapply(args, function(arg) {
> .arg <- arg # nice trick
> if (missing(.arg)) {
> "missing"
> } else {
> class(eval(arg, env))[1L]
> }
> }, character(1))
> defined.sig <- selectMethod(fun, target.sig)@defined
> help(paste0(fun.name <http://fun.name>
> <http://fun.name> <http://fun.name>,
> ",", paste(defined.sig,
>
> collapse=","), "-method"))
> }
>
> path_to_gff <- "my.gff"
> helpwith(import(path_to_gff))
>
> helpwith(rbind(DataFrame(____mtcars), DataFrame(mtcars)))
>
> But where should it go?
>
>
> Nice fix. It's a bug in ? so it would need to go into ? itself.
>
> The man page for ? (accessible with ?`?`) says:
>
> S4 Method Documentation:
>
> [...]
>
> There are two different ways to look for
> documentation on a
> particular method. The first is to supply the
> ‘topic’ argument in
> the form of a function call, omitting the ‘type’
> argument. The
> effect is to look for documentation on the method
> that would be
> used if this function call were actually evaluated.
> See the
> examples below. If the function is not a generic (no
> S4 methods
> are defined for it), the help reverts to
> documentation on the
> function name.
>
> Thanks,
> H.
>
>
>
>
>
> On Fri, Feb 21, 2014 at 11:17 AM, Hervé Pagès
> <hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>> wrote:
>
> Hi Gabriel,
>
>
> On 02/20/2014 05:03 PM, Gabriel Becker wrote:
>
> Herve,
>
> The help is correct (though possibly a bit
> pedantic),
> there is no
> method for that signature.
>
>
> But the dispatch mechanism is able to find one because
> 'import(path_to_gff)' *does* work. So the help
> maybe is correct
> but that doesn't really help the naive user.
>
> H.
>
>
> ?import("", "")
>
> works for me though
>
> ~G
>
>
> On Thu, Feb 20, 2014 at 4:51 PM, Hervé Pagès
> <hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>> wrote:
>
> On 02/20/2014 04:16 PM, Michael Lawrence
> wrote:
>
> There's also "?coverage(ga)", so the
> user can
> see what
> happens
> specifically for their object, without
> worrying about
> typing out
> the class.
>
>
> I was never lucky with this:
>
> > library(rtracklayer)
> > path_to_gff <- system.file("tests",
> "v1.gff",
> package =
> "rtracklayer")
> > ?import(path_to_gff)
> Error in .helpForCall(topicExpr,
> parent.frame()) :
> no documentation for function
> ‘import’ and
> signature
> ‘con =
> "character", format = "ANY", text = "ANY"’
> In addition: Warning message:
> In .helpForCall(topicExpr,
> parent.frame()) :
> no method defined for function
> ‘import’ and
> signature
> ‘con =
> "character", format = "ANY", text = "ANY"’
>
> H.
>
>
> At some point it would be neat to
> generate S4
> documentation at
> run-time.
> Just popup a browser and see every
> method that
> might be
> dispatched with
> a given object. In theory, the R help
> server would
> support this.
>
>
> On Thu, Feb 20, 2014 at 3:13 PM,
> Hervé Pagès
> <hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>>> wrote:
>
>
>
> On 02/20/2014 02:55 PM, Martin
> Morgan wrote:
>
> On 02/20/2014 02:32 PM,
> Hervé Pagès
> wrote:
>
> Hi Jesper,
>
> On 02/20/2014 02:13 PM,
> Jesper
> Gådin wrote:
>
> Very true that it is
> quite
> difficult
> to find the
> documentation when one
> is not aware of its
> existence :P
>
>
> Yeah, this has been a
> source of
> frustration for
> many people. And
> always a source of
> embarrassment
> (for us) when
> teaching our
> software
> to beginners.
>
> I've started to change
> this. In
> the upcoming
> version of BioC
> (2.14,
> scheduled for
> mid-April), when
> you'll do
> ?coverage,
> you'll
> get to
> choose between the 3 man
> pages that
> document coverage
> methods (there
> is one in IRanges, one in
> GenomicRanges,
> and one in
> GenomicAlignments).
>
> I want to generalize
> this to other
> generics that have
> methods spread
> across several packages
> (e.g.
> findOverlaps, the
> intra- and
> inter-range
> methods, etc...).
>
> Having to choose between
> several
> man pages
> every
> time you do
> e.g.
> ?findOverlaps is a minor
> annoyance
> compared to not
> being able to
> find the man page at
> all. (Note
> that if
> you already
> know
> where is
> your favorite man page,
> you'll be
> able to
> direct
> access it with
> e.g.
> ?GenomicRanges::findOverlaps). Nobody
> will
> ever need to use
> the insane
>
>
>
> ?`findOverlaps,GenomicRanges,__________GenomicRanges-method` to
>
>
>
>
>
> tab completion helps, so
> that you
> don't need
> to be totally
> insane, just
> insane enough to know to
> start with
>
> ?"cover<tab>
>
>
> and also insane enough to know which
> method you
> need to
> pick up amongst
> the 30+ methods listed by
> ?"findOverlaps<tab>
> Overwhelming!
>
> H.
>
>
>
> Martin
>
> open that man page
> again. Ever!
> (it will
> still work
> though...)
>
> Cheers,
> H.
>
>
> coverage() is fast and
> beautiful. Thanks!
>
> /Jesper
>
>
> On Wed, Feb 19, 2014
> at 9:21
> PM, Hervé
> Pagès
> <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>>
>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>
> <mailto:hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at fhcrc.org>>>>>>>
>
> wrote:
>
> Hi Jesper,
>
>
> On 02/19/2014
> 08:44 AM,
> Michael
> Lawrence
> wrote:
>
> On Wed, Feb
> 19, 2014
> at 8:39 AM,
> Jesper Gådin
>
> <jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>__>__>>wrote:
>
>
>
>
> Hi Michael,
>
> Herves
> suggestion will
> probably
> work for my
> use case, but if
> there
> are any
>
> smoother ways it
> would be
> preferable.
>
> The use
> case is
> as follows:
>
> 1)
> calculate
> strand specific
> coverage over
> a region from
> GAlignments
> object (or file)
>
> At the
> moment I
> read a
> file using
> readGAlignmentsFromBam()
> with
> tag="XS",
> then
> filter it
> on "flag" and
> "mapq". Then I
> subset the
> resulting
> GAlignments in
> a minus
> and a plus
> -strand object.
> Then I
> calculate
> coverage
> by my own
> coverage function which
> uses
> the cigar
>
> information in the
> GAlignments
> object. This
> function is the
> one using
>
> cigarToRleList()
> at the
> moment. As I
> understand the
>
> coverage() function
> from the
> GenomicAlignments/IRanges
> package
> does not take
> into
> account
> cigars,
> or does it?
>
>
> It does
> take the
> coverage
> into account;
> specifically to exclude
> the introns
> from
> coverage. I think
> there's also an
> option
> to exclude
> deletions.
>
>
> Unfortunately
> the man
> page is not
> easy to
> access
> (you need to do
>
> ?`coverage,GAlignments-method`____________), but
>
>
> it says:
>
> The methods for
> GAlignments and
> GAlignmentPairs
> objects do:
>
>
> coverage(grglist(x), ...)
>
> And if you do
> grglist() on a
> GAlignments or
> GAlignmentPairs
> objects, the
> ranges you get
> in the
> returned
> GRangesList
> object
> are calculated
> based
> on the CIGAR.
>
> Trust but
> verify. Here
> is how you
> can actually
> verify that
> coverage()
> does take the
> CIGAR into
> account:
>
>
> library(RNAseqData.HNRNPC.bam.____________chr14)
> gal <-
>
>
>
>
> readGAlignments(RNAseqData.____________HNRNPC.bam.chr14_____BAMFILES[__1])
>
>
>
> cig_op_table <-
> cigarOpTable(cigar(gal))
>
> First we pick up an
> alignment
> with an N in its
> CIGAR and do
> coverage()
> on it:
>
> > gal_with_N <-
> gal[which(cig_op_table[
> , "N"]
> != 0)[1]]
>
> > gal_with_N
> GAlignments
> with 1
> alignment and 0
> metadata columns:
>
> seqnames strand
> cigar qwidth
> start end
> width
>
> <Rle> <Rle>
> <character> <integer>
> <integer> <integer>
> <integer>
> [1]
> chr14 +
> 55M2117N17M 72
> 19650072 19652260
> 2189
> ngap
> <integer>
> [1] 1
> ---
> seqlengths:
>
> chr1
> chr10 ...
> chrY
>
> 249250621
> 135534747 ...
> 59373566
>
> >
> coverage(gal_with_N)$chr14
> integer-Rle
> of length
> 107349540 with 5 runs
> Lengths:
> 19650071
> 55
> 2117
> 17
> 87697280
> Values :
> 0
> 1
> 0
> 1
> 0
>
> Same thing with an
> alignment with
> an I in
> its CIGAR:
>
> > gal_with_I <-
> gal[which(cig_op_table[
> , "I"]
> != 0)[1]]
>
> > gal_with_I
> GAlignments
> with 1
> alignment and 0
> metadata columns:
>
> seqnames strand
> cigar qwidth
> start end
> width
>
> <Rle> <Rle>
> <character> <integer>
> <integer> <integer>
> <integer>
> [1]
> chr14 -
> 64M1I7M 72
> 19411677 19411747
> 71
> ngap
> <integer>
> [1] 0
> ---
> seqlengths:
>
> chr1
> chr10 ...
> chrY
>
> 249250621
> 135534747 ...
> 59373566
>
> >
> coverage(gal_with_I)$chr14
> integer-Rle
> of length
> 107349540 with 3 runs
> Lengths:
> 19411676
> 71 87937793 <tel:71%2087937793>
> <tel:71%2087937793>
> Values :
> 0
> 1
> 0
>
> Same thing with an
> alignment with
> a D in
> its CIGAR:
>
> > gal_with_D <-
> gal[which(cig_op_table[
> , "D"]
> != 0)[1]]
>
> > gal_with_D
> GAlignments
> with 1
> alignment and 0
> metadata columns:
>
> seqnames strand
> cigar qwidth
> start end
> width
>
> <Rle> <Rle>
> <character> <integer>
> <integer> <integer>
> <integer>
> [1]
> chr14 +
> 38M1D34M 72
> 19659063 19659135
> 73
> ngap
> <integer>
> [1] 0
> ---
> seqlengths:
>
> chr1
> chr10 ...
> chrY
>
> 249250621
> 135534747 ...
> 59373566
>
> >
> coverage(gal_with_D)$chr14
> integer-Rle
> of length
> 107349540 with 3 runs
> Lengths:
> 19659062
> 73
> 87690405
> Values :
> 0
> 1
> 0
>
> Seeing is
> believing,
>
> Cheers,
> H.
>
>
>
> I
> started to
> look at the
> applyPileups() in
> Rsamtools which I
> can get to
> calculate
> coverage using
> cigars,
> but not
> using the strand or
> flag
>
> information for
> filtering. That
> solution
> would start from a
> bam-file
> instead
> of a
> GAlignments
> object,
> and sure I
> can do the
>
> filtering outside R.
> But it
> would be very
> convenient to
> do it
> all from within R.
>
> If
> there are
> nice solutions
> starting from
> both a GAlignments
> and a
>
> bam-file it would be
> great! =)
>
> /Jesper
>
>
>
> On Tue,
> Feb 18,
> 2014 at
> 10:52 PM,
> Michael
> Lawrence <
> lawrence.michael at gene.com <mailto:lawrence.michael at gene.com>
> <mailto:lawrence.michael at gene.__com
> <mailto:lawrence.michael at gene.com>>
> <mailto:lawrence.michael at gene.
> <mailto:lawrence.michael at gene.>____com
> <mailto:lawrence.michael at gene.__com
> <mailto:lawrence.michael at gene.com>>>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.__>____com
> <mailto:lawrence.michael at gene.
> <mailto:lawrence.michael at gene.>____com
> <mailto:lawrence.michael at gene.__com
> <mailto:lawrence.michael at gene.com>>>>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__.__>____com
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.__>____com
> <mailto:lawrence.michael at gene.
> <mailto:lawrence.michael at gene.>____com
> <mailto:lawrence.michael at gene.__com
> <mailto:lawrence.michael at gene.com>>>>>
>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__>__.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__>__.__>____com
>
>
>
>
> <mailto:lawrence.michael at gene <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>>__.__>____com
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.
> <mailto:lawrence.michael at gene
> <mailto:lawrence.michael at gene>.__>____com
> <mailto:lawrence.michael at gene.
> <mailto:lawrence.michael at gene.>____com
> <mailto:lawrence.michael at gene.__com
> <mailto:lawrence.michael at gene.com>>>>>>> wrote:
>
> Hi
> Jesper,
>
>
> Would you be
> willing to
> volunteer your
> use case? As
>
> Herve hinted,
>
> cigarToRleList and
> friends are
> low-level helpers. There
> may
> be an easier
> way to
> achieve what
> you want,
> or an
> opportunity to
>
> improve things.
>
> Michael
>
>
> On
> Mon, Feb
> 17, 2014
> at 1:10
> AM, Jesper
> Gådin
>
> <jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>
>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>
> <mailto:jesper.gadin at gmail.com
> <mailto:jesper.gadin at gmail.com>__>__>__>__>__>>wrote:
>
>
>
>
> Hi,
>
>
> Have
> come across a
> cigar-vector
> that is problematic
>
> to process.
>
>
> #load
> package
>
>
> library(GenomicAlignments)
>
>
>
> #load
> data (see
> attached file)
>
>
>
>
> load("2014-02-17-cigarExample.____________rdata")
>
>
>
>
>
>
> #run
> function
> cigarToRleList
>
>
> cigarRle <-
>
> cigarToRleList(cigarExample)
>
>
> Error in
> .Call2("Rle_constructor",
> values, lengths,
>
> check,
> 0L, PACKAGE =
>
> "IRanges") :
>
> integer
> overflow while
> summing
> elements in
> 'lengths'
>
>
> sessionInfo()
>
>
> R Under
> development (unstable)
> (2013-11-13 r64209)
>
> Platform:
> x86_64-unknown-linux-gnu
> (64-bit)
>
>
> locale:
>
> [1]
> LC_CTYPE=en_US.UTF-8
> LC_NUMERIC=C
>
> [3]
> LC_TIME=en_US.UTF-8
> LC_COLLATE=en_US.UTF-8
>
> [5]
> LC_MONETARY=en_US.UTF-8
>
> LC_MESSAGES=en_US.UTF-8
>
> [7]
> LC_PAPER=en_US.UTF-8
> LC_NAME=C
>
> [9]
> LC_ADDRESS=C
> LC_TELEPHONE=C
>
> [11]
> LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
>
> attached
> base
> packages:
> [1]
> parallel stats
> graphics
> grDevices utils
>
> datasets methods
>
> [8] base
>
>
> other
> attached
> packages:
> [1]
> GenomicAlignments_0.99.18
> Rsamtools_1.15.26
> [3]
> Biostrings_2.31.12
> XVector_0.3.6
> [5]
> GenomicRanges_1.15.26
> IRanges_1.21.23
> [7]
> BiocGenerics_0.9.3
>
>
> loaded via a
> namespace
> (and not
> attached):
>
> [1]
> BatchJobs_1.1-1135
> BBmisc_1.5
>
> BiocParallel_0.5.8
>
> bitops_1.0-6
>
>
> [5]
> brew_1.0-6
> codetools_0.2-8
> DBI_0.2-7
>
> digest_0.6.4
>
>
> [9]
> fail_1.2
> foreach_1.4.1
>
> iterators_1.0.6
> plyr_1.8
>
>
--
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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319