My conjecture is that this is because while import can handle you not
passing in a format, it doesn't have a default value for the parameter, so
? has no way of knowing what the body of the function is going to put into
the format variable before it uses it.
~G
On Thu, Feb 20, 2014 at 5:03 PM, Gabriel Becker <gmbec...@ucdavis.edu>wrote:
> 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>>
>>>
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>>>
>>> ______________________________
>>> _____________________
>>> 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>>
>>>
>>>
>>> --
>>> 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
>
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
