[BioC] ggbio 1.12.0 autoplot() with txdb example is broken

Dan Tenenbaum dtenenba at fhcrc.org
Sat Apr 26 18:57:34 CEST 2014



Leonardo Collado Torres <lcollado at jhsph.edu> wrote:
>Is there any reason why ggbio 1.12.2 hasn't made it to BioC release?
>http://master.bioconductor.org/packages/release/bioc/html/ggbio.html
>still
>points to 1.12.0
>

It's failing to build:

http://www.bioconductor.org/checkResults/release/bioc-LATEST/ggbio/zin2-buildsrc.html

Dan

>
>On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>wrote:
>
>>
>>
>> ----- Original Message -----
>> > From: "Leonardo Collado Torres" <lcollado at jhsph.edu>
>> > To: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>> > Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Bioconductor mailing
>list" <
>> bioconductor at r-project.org>
>> > Sent: Wednesday, April 23, 2014 3:38:11 PM
>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
>broken
>> >
>> > Dang it, forgot again to send with my @jhsph.edu account. See below
>> > again >.<
>> >
>> > On the email topic, is it possible to be subscribed with 2 emails
>> > accounts to the BioC mailing list but only get emails with one? I
>> > believe that I have to choose to either get the daily digest or get
>a
>> > single for every message sent. If not, I'll probably just drop my
>> > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail
>I
>> > got (our university is pushing these mails).
>> >
>>
>> I don't know; you could try it. Another option would be to configure
>your
>> mail client with a filter to drop the undesired bioc emails.
>>
>> Dan
>>
>>
>> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres
>> > <lcollado at jhu.edu> wrote:
>> > > Hi Dan,
>> > >
>> > > I got RSwitch to work with a second installation of R 3.1.
>> > > Basically,
>> > > I downloaded the leopard tarball, expanded it, renamed the folder
>> > > 3.1
>> > > to 3.1patched (which is the version I downloaded, but well,
>> > > anything
>> > > except for 3.1 would work), compressed it again, and then
>expanded
>> > > it
>> > > at the root location.
>> > >
>> > > So it would be something like this:
>> > >
>> > > wget
>> > >
>>
>http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz
>> > > tar -xvf R-*gz
>> > > mv Library/Frameworks/R.framework/Versions/3.1
>> > > Library/Frameworks/R.framework/Versions/3.1patched
>> > > tar -cvzf Rlib.tgz Library
>> > > sudo tar fvxz Rlib.tgz -C /
>> > >
>> > > Then used RSwitch, and was able to install BioC-devel.
>> > >
>> > > I might try out your `renv` at a different time. It's great to
>know
>> > > that it exists =)
>> > >
>> > > Cheers,
>> > > Leo
>> > >
>> > >
>> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin
>> > > <tengfei.yin at sbgenomics.com> wrote:
>> > >> Hi Dan,
>> > >>
>> > >> It works like a charm, thanks!
>> > >>
>> > >> I use your method, then I changed /Library/Framework/ folder and
>> > >> R.Framework
>> > >> folder ownership to myself so I don't have to sudo it, then I
>just
>> > >> add alias
>> > >> to "emacs2" and "emacs3" to run your renv to switch the R first.
>> > >> This solves
>> > >> my problem.
>> > >>
>> > >> Try to customize variable for R hooks in emacs as alternative
>> > >> solution, but
>> > >> may need more time.
>> > >>
>> > >> Thanks again!
>> > >>
>> > >> Tengfei
>> > >>
>> > >>
>> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum
>> > >> <dtenenba at fhcrc.org> wrote:
>> > >>>
>> > >>> Hi Tengfei,
>> > >>>
>> > >>> ----- Original Message -----
>> > >>> > From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>> > >>> > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> > >>> > Cc: "Bioconductor mailing list" <bioconductor at r-project.org>,
>> > >>> > lcollado at jhu.edu
>> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM
>> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example
>> > >>> > is broken
>> > >>> >
>> > >>> >
>> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on
>the
>> > >>> > R 3.1?
>> > >>>
>> > >>> Yes, install two copies of R 3.1 and switch between them.
>> > >>>
>> > >>> > And do some sort of switch for bioc? The website you send to
>me
>> > >>> > also
>> > >>> > have a R-devel build, my plan is to install bioc 3.0 on
>R-devel
>> > >>> > and
>> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only
>to
>> > >>> > switch bioc, so that I could debug and maintain released and
>> > >>> > devel
>> > >>> > version.
>> > >>>
>> > >>> PLEASE don't use R-devel at all.
>> > >>>
>> > >>> Just use R-3.1.0.
>> > >>>
>> > >>> You can use the Rswitch app but as you point out it won't work
>> > >>> within
>> > >>> emacs.
>> > >>>
>> > >>> This is what I do:
>> > >>>
>> > >>> Every time I download a new version of R, I run its installer.
>> > >>> The
>> > >>> installer always puts it in
>> > >>>
>> > >>> /Library/Frameworks/R.framework
>> > >>>
>> > >>> So after I install each version of R, I rename the R.framework
>> > >>> directory
>> > >>> to something like
>> > >>> R.framework.bioc214_snowleopard
>> > >>>
>> > >>> And then I make a symlink from R.framework.bioc214_snowleopard
>to
>> > >>> R.framework.
>> > >>>
>> > >>> I have a little script at https://github.com/dtenenba/renv
>which
>> > >>> lets me
>> > >>> see what the various installed Rs are:
>> > >>>
>> > >>> $ renv
>> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0
>> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
>> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
>> > >>>
>> > >>> This tells me that the currently active R is nicknamed
>> > >>> "releaseMav" (this
>> > >>> means there is a link from
>> > >>> /Library/Frameworks/R.framework.releaseMav to
>> > >>> /Library/Frameworks/R.framework. It shows the versions, svn
>> > >>> revisions,
>> > >>> dates, and architectures of each version. (darwin10.8.0 is Snow
>> > >>> Leopard;
>> > >>> darwin13.1.0 is Mavericks).
>> > >>>
>> > >>> Note that in my nomenclature devel means BioC devel, not
>R-devel.
>> > >>>
>> > >>> So if I wanted to switch to the "develSL" version I would do:
>> > >>>
>> > >>> sudo renv develSL
>> > >>>
>> > >>> HTH
>> > >>> Dan
>> > >>>
>> > >>>
>> > >>>
>> > >>> >
>> > >>> >
>> > >>> >
>> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum <
>> > >>> > dtenenba at fhcrc.org >
>> > >>> > wrote:
>> > >>> >
>> > >>> >
>> > >>> >
>> > >>> > Hi Tengfei,
>> > >>> >
>> > >>> > ----- Original Message -----
>> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> > >>> >
>> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>> > >>> > > Cc: "Bioconductor mailing list" <
>bioconductor at r-project.org
>> > >>> > > >,
>> > >>> > > lcollado at jhu.edu
>> > >>> >
>> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM
>> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
>example
>> > >>> > > is
>> > >>> > > broken
>> > >>> > >
>> > >>> > >
>> > >>> >
>> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am
>still
>> > >>> > > a
>> > >>> > > newbie to OSX ... I got R-devel running and I will try
>> > >>> > > Rswitcher, I
>> > >>> > > also want to do that switch easily in emacs too.
>> > >>> > >
>> > >>> > >
>> > >>> >
>> > >>> > You don't want to use R-devel. Both BioC release (2.14) and
>> > >>> > BioC
>> > >>> > devel (3.0) are meant to work with R-3.1.0, the released
>> > >>> > version of
>> > >>> > R.
>> > >>> >
>> > >>> > I think the Rswitch app just sets a symbolic link, so you
>> > >>> > should be
>> > >>> > able to do that within emacs. Run it and see what it does to
>> > >>> > /Library/Frameworks/R.framework.
>> > >>> >
>> > >>> > Dan
>> > >>> >
>> > >>> >
>> > >>> > >
>> > >>> > > cheers
>> > >>> > >
>> > >>> > >
>> > >>> > > Tengfei
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> >
>> > >>> >
>> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum <
>> > >>> > > dtenenba at fhcrc.org
>> > >>> > > >
>> > >>> > > wrote:
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > > ----- Original Message -----
>> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> > >>> > >
>> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
>> > >>> > > > Cc: "Bioconductor mailing list" <
>> > >>> > > > bioconductor at r-project.org >,
>> > >>> > > > lcollado at jhu.edu
>> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM
>> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
>> > >>> > > > example is
>> > >>> > > > broken
>> > >>> > > >
>> > >>> > > >
>> > >>> > >
>> > >>> > > > Hi Dan,
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > So you mean I install R 3.1 for snow leopard and it
>should
>> > >>> > > > work?
>> > >>> > >
>> > >>> > > Yes.
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > > ? Is
>> > >>> > > > there a way to build from source using biocLite, like
>type
>> > >>> > > > =
>> > >>> > > > "source", this is what I got
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > > library(BiocInstaller)
>> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1),
>?biocLite
>> > >>> > > > for
>> > >>> > > > help
>> > >>> > > > > biocLite("GenomicRanges")
>> > >>> > > > BioC_mirror: http://bioconductor.org
>> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R
>> > >>> > > > version
>> > >>> > > > 3.1.0.
>> > >>> > > > Installing package(s) 'GenomicRanges'
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > package ‘GenomicRanges’ is available as a source package
>> > >>> > > > but not
>> > >>> > > > as
>> > >>> > > > a
>> > >>> > > > binary
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > Warning message:
>> > >>> > > > package ‘GenomicRanges’ is not available (for R version
>> > >>> > > > 3.1.0)
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > Just wondering is there a solution without re-install R
>for
>> > >>> > > > snow
>> > >>> > > > leopard. And what's the plan for maverick?
>> > >>> > > >
>> > >>> > >
>> > >>> > > You can do
>> > >>> > > biocLite("GenomicRanges", type="source")
>> > >>> > >
>> > >>> > > but you need to have the appropriate compilers, etc.
>> > >>> > >
>> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You
>can
>> > >>> > > have
>> > >>> > > multiple installations of R on your Mac and switch between
>> > >>> > > them
>> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or
>another
>> > >>> > > easy
>> > >>> >
>> > >>> >
>> > >>> > > mechanism.
>> > >>> > >
>> > >>> > > We are building packages for Mavericks now, we just have to
>> > >>> > > resolve
>> > >>> > > a
>> > >>> > > few build issues and test the resulting packages, we still
>> > >>> > > hope to
>> > >>> > > have them available by the end of the month. But since you
>> > >>> > > can
>> > >>> > > install the Snow Leopard build without needing to remove
>your
>> > >>> > > Mavericks build, you should do that.
>> > >>> > >
>> > >>> > > Dan
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > > >
>> > >>> > > > Thanks
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > Tengfei
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <
>> > >>> > > > dtenenba at fhcrc.org
>> > >>> > > > > wrote:
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > Hi Tengfei,
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > ----- Original Message -----
>> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
>> > >>> > > > > To: lcollado at jhu.edu
>> > >>> > > > > Cc: bioconductor at r-project.org
>> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM
>> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
>> > >>> > > > > example
>> > >>> > > > > is
>> > >>> > > > > broken
>> > >>> > > > >
>> > >>> > > > > btw, based on the error, let me try to debug it.
>> > >>> > > > >
>> > >>> > > > >
>> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin
>> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote:
>> > >>> > > > >
>> > >>> > > > > > Hi Leonardo,
>> > >>> > > > > >
>> > >>> > > > > > Frankly speaking, the vignette is still in progress,
>> > >>> > > > > > and
>> > >>> > > > > > there
>> > >>> > > > > > are
>> > >>> > > > > > some
>> > >>> > > > > > known bugs in ggbio I need to fix (still trying to
>find
>> > >>> > > > > > a
>> > >>> > > > > > time
>> > >>> > > > > > to
>> > >>> > > > > > do that
>> > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc
>> > >>> > > > > > 2.14 on
>> > >>> > > > > > my
>> > >>> > > > > > new MBP
>> > >>> > > > > > with OSX 10.9, but fails, probably binary build is
>not
>> > >>> > > > > > ready
>> > >>> > > > > > for
>> > >>> > > > > > maverick
>> > >>> > > > > > yet, maybe available by the end of April?
>> > >>> > > > > >
>> > >>> > > > > > Thanks for reporting the bug, I will keep you posted
>on
>> > >>> > > > > > this
>> > >>> > > > > > when
>> > >>> > > > > > I
>> > >>> > > > > > successfully get it on my laptop and start fixing the
>> > >>> > > > > > problems.
>> > >>> > > > > >
>> > >>> > > >
>> > >>> > > > You can install the Snow Leopard build of R and should
>have
>> > >>> > > > no
>> > >>> > > > problems, binary packages are available for that version.
>> > >>> > > > It will
>> > >>> > > > run fine on Mavericks.
>> > >>> > > >
>> > >>> > > > Dan
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > > > cheers
>> > >>> > > > > >
>> > >>> > > > > > Tengfei
>> > >>> > > > > >
>> > >>> > > > > >
>> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado
>> > >>> > > > > > Torres <
>> > >>> > > > > > lcollado at jhsph.edu > wrote:
>> > >>> > > > > >
>> > >>> > > > > >> Hello Tengfei + bioc list,
>> > >>> > > > > >>
>> > >>> > > > > >> From
>> > >>> > > > > >>
>> > >>> > > > > >>
>>
>http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
>> > >>> > > > > >> page 4 (complied on april 11 2014), the following
>> > >>> > > > > >> example
>> > >>> > > > > >> loads
>> > >>> > > > > >> to
>> > >>> > > > > >> an
>> > >>> > > > > >> error as shown below. I wasn't seeing this error
>> > >>> > > > > >> before
>> > >>> > > > > >> (aka,
>> > >>> > > > > >> last
>> > >>> > > > > >> week). The only guess that comes to mind is the
>recent
>> > >>> > > > > >> update
>> > >>> > > > > >> to
>> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to
>> > >>> > > > > >> be
>> > >>> > > > > >> related
>> > >>> > > > > >> from
>> > >>> > > > > >> the traceback() output, well... maybe it's related
>to
>> > >>> > > > > >> the
>> > >>> > > > > >> ignore.strand = TRUE part as described in the error.
>> > >>> > > > > >>
>> > >>> > > > > >> I'll create a GitHub issue just for completeness.
>> > >>> > > > > >>
>> > >>> > > > > >> Thank you,
>> > >>> > > > > >> Leonardo
>> > >>> > > > > >>
>> > >>> > > > > >> > library(ggbio)
>> > >>> > > > > >> ## Removed the output, nothing out of ordinary
>> > >>> > > > > >>
>> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> > >>> > > > > >> ## Removed the output
>> > >>> > > > > >>
>> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>> > >>> > > > > >> > data(genesymbol, package = "biovizBase")
>> > >>> > > > > >> > p.txdb <- autoplot(txdb, which =
>> > >>> > > > > >> > genesymbol["BRCA1"])
>> > >>> > > > > >> Aggregating TranscriptDb...
>> > >>> > > > > >> Parsing transcripts...
>> > >>> > > > > >> Parsing exons...
>> > >>> > > > > >> Parsing cds...
>> > >>> > > > > >> Parsing utrs...
>> > >>> > > > > >> ------exons...
>> > >>> > > > > >> ------cdss...
>> > >>> > > > > >> ------introns...
>> > >>> > > > > >> ------utr...
>> > >>> > > > > >> aggregating...
>> > >>> > > > > >> Done
>> > >>> > > > > >> Constructing graphics...
>> > >>> > > > > >> Error in sapply(listData, function(Xi)
>> > >>> > > > > >> extends(class(Xi),
>> > >>> > > > > >> elementTypeX)) :
>> > >>> > > > > >> error in evaluating the argument 'X' in selecting a
>> > >>> > > > > >> method
>> > >>> > > > > >> for
>> > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n,
>> > >>> > > > > >> ignore.strand
>> > >>> > > > > >> =
>> > >>> > > > > >> TRUE))) :
>> > >>> > > > > >> error in evaluating the argument 'x' in selecting a
>> > >>> > > > > >> method
>> > >>> > > > > >> for
>> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused
>> > >>> > > > > >> argument
>> > >>> > > > > >> (ignore.strand = TRUE)
>> > >>> > > > > >>
>> > >>> > > > > >> > traceback()
>> > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi),
>> > >>> > > > > >> elementTypeX))
>> > >>> > > > > >> 14: .updateCompressedList(X,
>lapply_CompressedList(X,
>> > >>> > > > > >> FUN,
>> > >>> > > > > >> ...))
>> > >>> > > > > >> 13: endoapply(obj.lst, function(x) {
>> > >>> > > > > >> if (!is.null( group.name )) {
>> > >>> > > > > >> if (!group.selfish) {
>> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>> > >>> > > > > >> TRUE)))
>> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>> > >>> > > > > >> width(irs) +
>> > >>> > > > > >> extend.size)
>> > >>> > > > > >> irs.new <- sort(irs.new)
>> > >>> > > > > >> .lvs <- disjointBins(irs.new)
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> .lvs[as.character(values(x)[,
>> > >>> > > > > >> group.name ])]
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> else {
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> as.numeric(as.factor(values(x)[,
>> > >>> > > > > >> group.name ]))
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> }
>> > >>> > > > > >> else {
>> > >>> > > > > >> irs <- ranges(x)
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> as.numeric(disjointBins(resize(irs,
>> > >>> > > > > >> fix = "center", width = width(irs) +
>> > >>> > > > > >> extend.size)))
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> })
>> > >>> > > > > >> 12: endoapply(obj.lst, function(x) {
>> > >>> > > > > >> if (!is.null( group.name )) {
>> > >>> > > > > >> if (!group.selfish) {
>> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ])
>> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
>> > >>> > > > > >> TRUE)))
>> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width =
>> > >>> > > > > >> width(irs) +
>> > >>> > > > > >> extend.size)
>> > >>> > > > > >> irs.new <- sort(irs.new)
>> > >>> > > > > >> .lvs <- disjointBins(irs.new)
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> .lvs[as.character(values(x)[,
>> > >>> > > > > >> group.name ])]
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> else {
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> as.numeric(as.factor(values(x)[,
>> > >>> > > > > >> group.name ]))
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> }
>> > >>> > > > > >> else {
>> > >>> > > > > >> irs <- ranges(x)
>> > >>> > > > > >> values(x)$stepping <-
>> > >>> > > > > >> as.numeric(disjointBins(resize(irs,
>> > >>> > > > > >> fix = "center", width = width(irs) +
>> > >>> > > > > >> extend.size)))
>> > >>> > > > > >> x
>> > >>> > > > > >> }
>> > >>> > > > > >> })
>> > >>> > > > > >> 11: .local(obj, ...)
>> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id",
>> > >>> > > > > >> group.selfish =
>> > >>> > > > > >> FALSE,
>> > >>> > > > > >> fix = "start", extend.size = es)
>> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id",
>group.selfish
>> > >>> > > > > >> =
>> > >>> > > > > >> FALSE,
>> > >>> > > > > >> fix = "start", extend.size = es)
>> > >>> > > > > >> 8: .local(data, ...)
>> > >>> > > > > >> 7: (function (data, ...)
>> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object
>> > >>> > > > > >> of
>> > >>> > > > > >> class
>> > >>> > > > > >> "TranscriptDb">,
>> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
>> > >>> > > > > >> "alignment",
>> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label =
>> > >>> > > > > >> TRUE,
>> > >>> > > > > >> which = <S4 object of class "GRanges">, list())
>> > >>> > > > > >> 6: (function (data, ...)
>> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object
>> > >>> > > > > >> of
>> > >>> > > > > >> class
>> > >>> > > > > >> "TranscriptDb">,
>> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
>> > >>> > > > > >> "alignment",
>> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label =
>> > >>> > > > > >> TRUE,
>> > >>> > > > > >> which = <S4 object of class "GRanges">, list())
>> > >>> > > > > >> 5: do.call(geom_alignment, args.res)
>> > >>> > > > > >> 4: do.call(geom_alignment, args.res)
>> > >>> > > > > >> 3: .local(object, ...)
>> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"])
>> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"])
>> > >>> > > > > >>
>> > >>> > > > > >>
>> > >>> > > > > >> > sessionInfo()
>> > >>> > > > > >> R version 3.1.0 (2014-04-10)
>> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> > >>> > > > > >>
>> > >>> > > > > >> locale:
>> > >>> > > > > >> [1]
>> > >>> > > > > >>
>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> > >>> > > > > >>
>> > >>> > > > > >> attached base packages:
>> > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets
>> > >>> > > > > >> methods base
>> > >>> > > > > >>
>> > >>> > > > > >> other attached packages:
>> > >>> > > > > >> [1] XVector_0.4.0
>> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
>> > >>> > > > > >> GenomicFeatures_1.16.0
>> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0
>> > >>> > > > > >> GenomicRanges_1.16.2
>> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3
>> > >>> > > > > >> ggbio_1.12.0
>> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0
>> > >>> > > > > >>
>> > >>> > > > > >> loaded via a namespace (and not attached):
>> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5
>> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0
>> > >>> > > > > >> Biostrings_2.32.0
>> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6
>> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2
>> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
>> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4
>> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2
>> > >>> > > > > >> Formula_1.1-1
>> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0
>> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2
>> > >>> > > > > >> Hmisc_3.14-4
>> > >>> > > > > >> iterators_1.0.7 labeling_0.2
>> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31
>> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1
>> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1
>> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2
>> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4
>> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2
>> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0
>> > >>> > > > > >> stringr_0.6.2
>> > >>> > > > > >> survival_2.37-7 tools_3.1.0
>> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1
>> > >>> > > > > >> zlibbioc_1.10.0
>> > >>> > > > > >> >
>> > >>> > > > > >>
>> > >>> > > > > >
>> > >>> > > > > >
>> > >>> > > > > >
>> > >>> > > > > > --
>> > >>> > > > > > Tengfei Yin, PhD
>> > >>> > > > > > Seven Bridges Genomics
>> > >>> > > > > > sbgenomics.com
>> > >>> > > > > > 625 Mt. Auburn St. Suite #208
>> > >>> > > > > > Cambridge, MA 02138
>> > >>> > > > > > (617) 866-0446
>> > >>> > > > > >
>> > >>> > > > >
>> > >>> > > > >
>> > >>> > > > >
>> > >>> > > > > --
>> > >>> > > > > Tengfei Yin, PhD
>> > >>> > > > > Seven Bridges Genomics
>> > >>> > > > > sbgenomics.com
>> > >>> > > > > 625 Mt. Auburn St. Suite #208
>> > >>> > > > > Cambridge, MA 02138
>> > >>> > > > > (617) 866-0446
>> > >>> > > > >
>> > >>> > > > > [[alternative HTML version deleted]]
>> > >>> > > > >
>> > >>> > > > > _______________________________________________
>> > >>> > > > > Bioconductor mailing list
>> > >>> > > > > Bioconductor at r-project.org
>> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > >>> > > > > Search the archives:
>> > >>> > > > >
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> > >>> > > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > --
>> > >>> > > >
>> > >>> > > >
>> > >>> > > > Tengfei Yin, PhD
>> > >>> > > > Seven Bridges Genomics
>> > >>> > > > sbgenomics.com
>> > >>> > > > 625 Mt. Auburn St. Suite #208
>> > >>> > > > Cambridge, MA 02138
>> > >>> > > > (617) 866- 0446
>> > >>> > > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > >
>> > >>> > > --
>> > >>> > >
>> > >>> > >
>> > >>> > > Tengfei Yin, PhD
>> > >>> > > Seven Bridges Genomics
>> > >>> > > sbgenomics.com
>> > >>> > > 625 Mt. Auburn St. Suite #208
>> > >>> > > Cambridge, MA 02138
>> > >>> > > (617) 866- 0446
>> > >>> > >
>> > >>> >
>> > >>> >
>> > >>> >
>> > >>> >
>> > >>> > --
>> > >>> >
>> > >>> >
>> > >>> > Tengfei Yin, PhD
>> > >>> > Seven Bridges Genomics
>> > >>> > sbgenomics.com
>> > >>> > 625 Mt. Auburn St. Suite #208
>> > >>> > Cambridge, MA 02138
>> > >>> > (617) 866- 0446
>> > >>> >
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Tengfei Yin, PhD
>> > >> Seven Bridges Genomics
>> > >> sbgenomics.com
>> > >> 625 Mt. Auburn St. Suite #208
>> > >> Cambridge, MA 02138
>> > >> (617) 866-0446
>> >
>>



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