[Bioc-devel] cigarToRleList fails

Hervé Pagès hpages at fhcrc.org
Sat Feb 22 21:26:49 CET 2014


Thanks Michael.

Do you think it would be sensible to offer a similar fix for
selectMethod?

   > setGeneric("f", function(x, y) standardGeneric("f"))
   > setMethod("f", c("numeric", "missing"), function(x, y) x)
   > selectMethod("f", "numeric")
   Error in selectMethod("f", "numeric") :
     no method found for signature numeric, ANY

In a perfect world,

   generic(arg)
   selectMethod(generic, class(arg))
   ?generic(arg)

should behave consistently.

The ?import(path_to_gff) error I reported earlier was actually
inspired by a sad experience I had in the past where I was trying
to use selectMethod("import", ...) to find out what particular
method was being called (I needed to see the code).

Thanks,
H.


On 02/22/2014 05:59 AM, Michael Lawrence wrote:
> Translated it into a patch against R, submitted here:
> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15680
>
>
> On Fri, Feb 21, 2014 at 2:53 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> wrote:
>
>
>
>     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> <http://fun.name> <- deparse(expr[[1L]])
>             if (!isGeneric(fun.name <http://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> <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>
>         <mailto: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>>
>                  <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 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>>>
>                           <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:
>
>
>
>                                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>>>>
>                                            <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
>         <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>__>__>__>
>
>         <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
>         <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>>>>
>
>                  <mailto:lawrence.michael at gene
>         <mailto:lawrence.michael at gene> <mailto:lawrence.michael at gene
>         <mailto:lawrence.michael at gene>>__.
>                           <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>.
>                  <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>__>__>__>
>
>                  <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
>         <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
>
>
>
>
>           _________________________________________________________
>
>
>         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>>
>                  <mailto:Bioc-devel at r-project.
>         <mailto: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
>         <mailto:Bioc-devel at r-project>.
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.>______org
>                           <mailto:Bioc-devel at r-project.
>         <mailto: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
>         <mailto:Bioc-devel at r-project>
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>>.
>                           <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>>.__>______org
>
>
>                                            <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.>______org
>                           <mailto:Bioc-devel at r-project.
>         <mailto:Bioc-devel at r-project.>____org
>                  <mailto:Bioc-devel at r-project.__org
>         <mailto:Bioc-devel at r-project.org>>>>> mailing list
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>                  version
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>           _________________________________________________________
>
>
>         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>>
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>         <mailto: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
>         <mailto:Bioc-devel at r-project>.
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.>______org
>                           <mailto:Bioc-devel at r-project.
>         <mailto: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
>         <mailto:Bioc-devel at r-project>
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>>.
>                           <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>>.__>______org
>
>
>                                            <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.
>                  <mailto:Bioc-devel at r-project
>         <mailto:Bioc-devel at r-project>.>______org
>                           <mailto:Bioc-devel at r-project.
>         <mailto:Bioc-devel at r-project.>____org
>                  <mailto:Bioc-devel at r-project.__org
>         <mailto:Bioc-devel at r-project.org>>>>>
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>                  <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: 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>>>>
>                                            <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
>         <mailto:hpages at fhcrc.org>>>>>
>
>
>                                                 Phone: (206) 667-5791
>         <tel:%28206%29%20667-5791>
>                  <tel:%28206%29%20667-5791>
>                           <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>
>         <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>>>
>                           <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>>>>
>                                Phone: (206) 667-5791
>         <tel:%28206%29%20667-5791> <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>
>                           <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>
>
>                       _____________________________________________________
>         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>>
>                  <mailto:Bioc-devel at r-project.
>         <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
>         <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>>>
>
>
>
>
>                  --
>                  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>
>         <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>
>
>
>
>     --
>     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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