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


On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

>
>
> ----- Original Message -----
> > From: "Leonardo Collado Torres" <lcollado@jhsph.edu>
> > To: "Tengfei Yin" <tengfei.yin@sbgenomics.com>
> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing list" <
> bioconductor@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@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@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@fhcrc.org> wrote:
> > >>>
> > >>> Hi Tengfei,
> > >>>
> > >>> ----- Original Message -----
> > >>> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com>
> > >>> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> > >>> > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>,
> > >>> > lcollado@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@fhcrc.org >
> > >>> > wrote:
> > >>> >
> > >>> >
> > >>> >
> > >>> > Hi Tengfei,
> > >>> >
> > >>> > ----- Original Message -----
> > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com >
> > >>> >
> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org >
> > >>> > > Cc: "Bioconductor mailing list" < bioconductor@r-project.org
> > >>> > > >,
> > >>> > > lcollado@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@fhcrc.org
> > >>> > > >
> > >>> > > wrote:
> > >>> > >
> > >>> > >
> > >>> > >
> > >>> > >
> > >>> > >
> > >>> > > ----- Original Message -----
> > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com >
> > >>> > >
> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org >
> > >>> > > > Cc: "Bioconductor mailing list" <
> > >>> > > > bioconductor@r-project.org >,
> > >>> > > > lcollado@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@fhcrc.org
> > >>> > > > > wrote:
> > >>> > > >
> > >>> > > >
> > >>> > > > Hi Tengfei,
> > >>> > > >
> > >>> > > >
> > >>> > > > ----- Original Message -----
> > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com >
> > >>> > > > > To: lcollado@jhu.edu
> > >>> > > > > Cc: bioconductor@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@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@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@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
> >
>

	[[alternative HTML version deleted]]

