Herve,
The help is correct (though possibly a bit pedantic), there is no method
for that signature.
?import("", "")
works for me though
~G
On Thu, Feb 20, 2014 at 4:51 PM, Hervé Pagès <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>> 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>>>
>> 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>__>>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.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>__>>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>> 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>>
>>
>>
>>
>>
>>
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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>>
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>>
>>
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>> <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>>
>>
>> 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>
>>
>>
>>
> --
> 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
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
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