[Bioc-devel] cigarToRleList fails
Hervé Pagès
hpages at fhcrc.org
Fri Feb 21 23:53:54 CET 2014
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> <- deparse(expr[[1L]])
> if (!isGeneric(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>, ",", 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>> 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>>> 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>>>> 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>>>>>
> 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>__>__>__>>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.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>>>>> 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>__>__>__>>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
>
>
>
> _______________________________________________________
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>
> --
> 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
>
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> <tel:%28206%29%20667-1319>
> <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: 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>>>
> 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: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> <mailto:hpages at fhcrc.org <mailto:hpages at 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>
>
> ___________________________________________________
> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> <mailto:Bioc-devel at r-project.__org
> <mailto:Bioc-devel at r-project.org>> mailing list
> https://stat.ethz.ch/mailman/____listinfo/bioc-devel
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> <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: hpages at fhcrc.org <mailto:hpages at 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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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