On Fri, Feb 21, 2014 at 2:03 PM, Gabriel Becker <gmbec...@ucdavis.edu>wrote:
> Michael,
>
> Why not just load the help page for the function if it's not a generic
> instead of throwing an error?
>
> Also, it's possible that it skipping missing arguments and going straight
> to any is a bug in help, rather than the designed behavior. Perhaps we
> should check?
>
>
Agree on both points. Just a quick proof of concept.
> ~G
>
>
> On Fri, Feb 21, 2014 at 2:01 PM, Michael Lawrence <
> lawrence.mich...@gene.com> 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 <- 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>
>>>>
>>>>
>>>> <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>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> [[alternative HTML version
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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
>>>
>>
>>
>
>
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
>
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