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 <- deparse(expr[[1L]])
if (!isGeneric(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@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, ",", 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?
On Fri, Feb 21, 2014 at 11:17 AM, Hervé Pagès <hpa...@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 <hpa...@fhcrc.org
>> <mailto:hpa...@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 <hpa...@fhcrc.org
>> <mailto:hpa...@fhcrc.org>
>> <mailto:hpa...@fhcrc.org <mailto:hpa...@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
>> <hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>
>> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>>
>> <mailto:hpa...@fhcrc.org
>> <mailto:hpa...@fhcrc.org> <mailto:hpa...@fhcrc.org
>> <mailto:hpa...@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.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>__>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@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>
>> 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.mich...@gene.com <mailto:lawrence.mich...@gene.com>
>> <mailto:lawrence.michael@gene.__com
>> <mailto:lawrence.mich...@gene.com>>
>> <mailto:lawrence.michael@gene.
>> <mailto:lawrence.michael@gene.>____com
>>
>>
>> <mailto:lawrence.michael@gene.__com
>> <mailto:lawrence.mich...@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.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>__>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@gmail.com>
>> <mailto:jesper.ga...@gmail.com
>> <mailto:jesper.ga...@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
>>
>> [13] RSQLite_0.11.4
>> sendmailR_1.1-2
>> stats4_3.1.0
>> tools_3.1.0
>>
>> [17] zlibbioc_1.9.0
>>
>>
>>
>> _____________________________________________________
>>
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
>> <mailto:Bioc-devel@r-project.__org
>> <mailto:Bioc-devel@r-project.org>>
>>
>> <mailto:Bioc-devel@r-project.
>> <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>
>>
>>
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>> <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
>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>>
>>
>>
>>
>>
>>
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>>
>>
>>
>>
>>
>> _____________________________________________________
>>
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
>> <mailto:Bioc-devel@r-project.__org
>> <mailto:Bioc-devel@r-project.org>>
>> <mailto:Bioc-devel@r-project.
>> <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>>
>>
>>
>>
>> <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>>
>> <mailto: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>
>> <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319
>> <tel:%28206%29%20667-1319> <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>
>> <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>
>>
>> _________________________________________________
>> 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>
>>
>>
>>
>>
>> --
>> Gabriel Becker
>> Graduate Student
>> Statistics Department
>> University of California, Davis
>>
>
> --
> 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
>
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