Hi,
When I use the 'filterVcf' function to process a VCF file in chunks, the
output file contains as many copies of the header as there are
chunks. Consider the example, adapted from the 'filterVcf' man page:
library(VariantAnnotation)
fl <- system.file(package = "VariantAnnotation", "extdat
this further
- added a 'verbose' arg to readVcf(); when TRUE fields found in header
are printed
Valerie
On 07/16/2015 02:35 AM, Julian Gehring wrote:
Hi,
In recent versions of 'VariantAnnotation', the 'readVcf' function prints
information a
Hi Dan,
Thanks you for the very quick fix!
Best wishes
Julian
On Thu, Jul 16, 2015 at 19:08, Dan Tenenbaum wrote:
- Original Message -
From: "Julian Gehring"
To: bioc-devel@r-project.org (mailto:bioc-devel@r-project.org)
Sent: Thursday, July 16, 2015 2:22:53 AM
Subject: [
Hi,
In recent versions of 'VariantAnnotation', the 'readVcf' function prints
information about the header lines:
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
shows
found header lines for 3 ‘fixed’ fields: ALT, QUAL, FILTER
found heade
Hi,
It seems that 'ggbio' is affected by the major rewrite of 'gridExtra'
(2.0.0) that was released a few days ago
(http://cran.r-project.org/web/packages/gridExtra/news.html).
library(ggbio)
yields
Error : object ‘latticeGrob’ is not exported by 'namespace:gridExtra'
Error: package or na
;> Looks like an issue when expand()ing the VCF. Maybe Val could take a look?
>>
>> On Wed, Dec 3, 2014 at 7:39 AM, Julian Gehring
>> wrote:
>>
>>> Hi,
>>>
>>> The conversion from a 'VCF' to 'VRanges' object fails if an
I guess Vince was more thinking of a GUI for constructing the ScanVcfParam
object itself, given a VCF file.
Have a look at
https://gist.github.com/julian-gehring/978ff86691bd87e95daf
(https://gist.github.com/julian-gehring/978ff86691bd87e95daf)
Quick and dirty prototype, a shiny app to
Hi,
Assume that we have two variants from two samples at the same locus,
stored in a 'VRanges' or 'VCF' object:
library(VariantAnnotation)
vr = VRanges("1", IRanges(c(10, 10), width = 1),
ref = c("C", "C"), alt = c("A", "G"),
sampleNames = c("S1", "S2"))
vcf = as(vr, "VCF")
If we
Hi,
Can we harmonize the default parameters for =ScanVcfParam= and
=VRangesScanVcfParam=? It even seems that we could drop
=VRangesScanVcfParam= since it is mainly a wrapper for =ScanVcfParam=.
Currently, the defaults for importing fields from a VCF are:
ScanVcfParam: fixed = character(), inf
Hi,
The conversion from a 'VCF' to 'VRanges' object fails if an INFO field
with multiple values for different ALT alleles is present:
Here an example VCF entry for which this fails (line 71151250 in
'ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz'
, taken from
ftp://ftp.1000g
knownGene)
However, this does not work for the non-toplevel chrs, e.g.:
'HSCHR19KIR_RP5_B_HAP_CTG3_1' does not have a corresponding sequence in
the 'TxDb.Hsapiens.UCSC.hg38.knownGene' (and also won't be converted).
Best
Julian
Julian Gehring (12/02/14 15:44):
&g
Ignore my comment about the naming convention.
On Tue, Dec 2, 2014 at 15:45, Julian Gehring wrote:The naming of the
chromosomes has been harmonized between UCSC and GRCh with the new release, so
there should be no need for two versions at the genome level.
[[alternative HTML version
Hi Raffaele,
You can find it under the name
BSgenome.Hsapiens.NCBI.GRCh38
http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html
(http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html)
The naming of the chr
Hi,
some/many of the package build RSS feeds [1] don't receive updates. For
example,
http://bioconductor.org/rss/build/packages/DESeq2.rss (from
2014-11-04)
http://bioconductor.org/rss/build/packages/BiocInstaller.rss (from
2014-10-15)
report package builds as broken, although the cu
Hi January,
On Fri, Nov 14, 2014 at 11:52, January Weiner wrote:
2) Another problem I have is the testing package on other platforms. I
do not have a Windows machine to test my package. Could someone help
me and test my package (build, check and BiocCheck) on Windows and
MacOS? Otherwise -- how d
Hi,
Can we embed the posting guide
(http://bioconductor.org/help/support/posting-guide/) directly in the
post form of the support forum? This way it should get maximal
visibility.
Best
Julian
___
Bioc-devel@r-project.org mailing list
https://stat.ethz
Hi Andzrej,
thank you, I see your point but I'm afraid I must disagree with you.
I've had this situation numerous times that I have added/fixed
something in the devel branch of a package and had to advice the users
to use this latest version. Needless to say, they were typically using
the release b
ackage" gets installed, by manually using an
inappropriate
tarball.
wrong documentation is not so easy but the doc on the devel branch might
have a different tooltip cautioning the readers to be sure they want to
read the doc on the devel version.
On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehrin
Hi,
Can we make the package websites for the devel and release version of a
package more distinguishable?
To elaborate on this: In the past, I have seen several users having
problems with using bioconductor because they ended up on the wrong page
(mostly the devel page when they would have n
]
https://github.com/epiviz/epivizr-release [3]
Also available on svn and will be available on next build.
Thanks!
Hector
PS. Let me know how things go!
On Wed, Jun 4, 2014 at 2:41 PM, Julian Gehring
wrote:
Hi,
When I try to start epivizr with a defined region of interest, the
region is
Hi,
When I try to start epivizr with a defined region of interest, the region is
always mapped to the default chromosome 11.
library(epivizr)
mz = startEpiviz(chr = "chr2", start = 1e5, end = 2e5)
yields the URL
http://epiviz.cbcb.umd.edu/index.php?websocket-host[]=ws://localhost:7312&debug=fa
Hi,
If I want to bind two GRanges object with a matrix in the meta columns,
the concatenation of the two fails in bioc-stable (GenomicRanges 1.16.3)
and bioc-devel (GenomicRanges 1.17.13) with:
'''
Error in validObject(.Object) :
invalid class “GRanges” object: number of rows in DataTable
QDNAseq-relase/master), but it’s enough to make me fairly
indifferent to the branch limitation of the bridge.
Ilari
On 14.5.2014, at 15.26, Julian Gehring mailto:julian.gehr...@embl.de>> wrote:
> Hi,
>
> Are there plans for the awesome git-svn bridge to a
Hi,
Are there plans for the awesome git-svn bridge to allow the tracking of
devel and releases in different branches of the same git repository?
Currently, one has to create different repos for devel and release (see
http://bioconductor.org/developers/how-to/git-svn/).
Best wishes
Julian
__
;
>> >>
>> >> On Mon, May 5, 2014 at 12:11 PM, Michael Lawrence
> >>> wrote:
>> >>
>> >>> In my opinion, granges() is not very clear as to the
intent. The mcols are
>> >>> part of the GRanges, so why
Hi,
On 05.05.2014 16:22, Martin Morgan wrote:
generalize as setMcols, like setNames? setMcols(x, NULL)
How about Tim's original suggestion, to add a 'granges' method that
works on a 'GRanges' input? The current definition
granges(x, use.mcols=FALSE, ...)
seem suited for this.
Best wishes
Hi Tim,
I was looking for a similar function a while ago, and created the
'grangesPlain' function in 'SomaticSignatures':
grangesPlain <-
function (x)
{
mcols(x) = NULL
x = as(x, "GRanges")
return(x)
}
It removes the metadata columns, as Michael described. Further, it
performs a
Hi,
With the latest bioc-devel, the convertion of XStringSets within a
DataFrame to a data.frame behaves strangely:
library(Biostrings)
dss = DNAStringSet(c("ACT", "AAA"))
DF = DataFrame(dss)
as(DF, "data.frame")
In the latest bioc-devel, this splits the strings:
dss.group dss.gro
Hi,
For most problems discussed here, it seems that having a fixed version
of package is sufficient rather than a specific version. If the idea of
a snapshot with each bioc release would work (which still means one
version per package), so would requiring that version within the package
(one
Hi,
For a "more general solution" one could think of specifying the version
of critical packages in the 'description' file and having a 'biocLite'
function that installs the specific version from CRAN. See e.g. the
'devtools::install_version' function for installing older packages from
the C
Related to this, running 'biocLite("BiocUpgrade")' with an bioc-3.0
triggers an upgrade to bioc-3.1 which is non-existing.
Best wishes
Julian
On 22.04.2014 14:38, Julian Gehring wrote:
Hi,
Alejandro and I digged deeper into this:
The bug I described before as caus
and FALSE for devel.
Best wishes
Julian
On 17.04.2014 18:50, Steve Lianoglou wrote:
HI,
On Thu, Apr 17, 2014 at 7:09 AM, Julian Gehring wrote:
Hi,
When I run
source("http://bioconductor.org/biocLite.R";)
biocLite("BiocUpgrade")
on a stable R-3.1.0 with bioc 2.14
Hi,
When I run
source("http://bioconductor.org/biocLite.R";)
biocLite("BiocUpgrade")
on a stable R-3.1.0 with bioc 2.14 already installed, bioc wants to
upgrade to bioc 3.0 (devel):
Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help
Upgrade all packages to Bioconductor
Hi Ushi,
> Thanks for your reply. I spoke to the original author. He has some
> concerns about wrapping everything into separate functions.
How you design the functions is in the end up to you. Generally, in an
R package there should not be the need for calling 'source'.
> We are dealing with
Hi Ushi,
For an R package, you would like to get rid of the 'source' calls
completely. You would want to design your code such that different
tasks are represented as different functions. If you have all these
functions in the 'R' directory of your package, you can access them
easily and do not
No, it's down again (for https://github.com/julian-gehring/Rariant and
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rariant/).
On 08/04/14 10:18, Julian Gehring wrote:
> Hi Dan,
>
> Thanks, it is working fine now. Is it clear what was the cause of this?
>
>
Hi Dan,
Thanks, it is working fine now. Is it clear what was the cause of this?
Best wishes
Julian
On 07/04/14 19:11, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Julian Gehring"
>> To: "Dan Tenenbaum"
>> Cc: bioc-devel@
Hi Dan,
It is still not working for me (packages 'Rariant' and
'SomaticSignatures'), both for pushed commits and manually triggering
the hook.
Best wishes
Julian
On 07/04/14 18:55, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: &q
Hi,
The git-svn bridge seem to be down. Pushing commits from github to the
bioc svn fail with "We couldn’t deliver this payload: Service Timeout"
and 'http://gitsvn.bioconductor.org/git-push-hook' is also not reachable.
Best wishes
Julian
___
Bioc-dev
Hi,
BiocCheck:::getVigSources check for vignette source files in the
'vignettes' directory. Currently, this includes 'Rmd', 'Rnw', 'Rrst'.
Shouldn't this also include 'rhtml' and 'rtex' which are valid source
formats (see http://yihui.name/knitr/demo/minimal/).
Best wishes
Julian
__
Hi Michael,
Thanks, works all fine now.
Best wishes
Julian
On 28/03/14 22:05, Michael Lawrence wrote:
> Thanks, should be resolved in 1.23.20 (devel).
>
>
> On Fri, Mar 28, 2014 at 8:09 AM, Julian Gehring <mailto:julian.gehr...@embl.de>> wrote:
>
> Hi,
&
Hi,
Exporting a GRanges object to the 'bigwig' format with rtracklayer fails
if not all seqlevels are used:
#+BEGIN_SRC R
library(rtracklayer)
library(GenomicRanges)
## example data
example(GRanges)
lg = reduce(unstrand(longGR))
lg$score = 1:6
## full one works
export(lg, tempfi
Hi Ryan,
Thank you for the detailed bug report and already providing a fix for
this. I have added your patch to 'les_1.13.2' and pushed it to
bioc-devel, the updated build should become available soon.
I'll do some more tests within the next days, and then also update
bioc-release. If you need
Hi Valerie,
I would consider G>C an SNV, G>TT not. But I assume that there exists
no clear consensus on this. How about a flag that let's the second pass
as SNV optionally, so everybody can get what one needs?
Best wishes
Julian
On 18/03/14 18:36, Valerie Obenchain wrote:
> Hi,
>
> I've adde
; Hi,
>
> To me it sounds like what I am expecting, from a R base point of view.
>
> x<-1:5
> names(x)<-letters[1:5]
> i<-'f'
> x[i]
>
> Best,
> Dan
>
> On Thu, 2014-02-27 at 13:49 +0100, Julian Gehring wrote:
>> Hi,
>>
>
i, "GRanges")')
with a non-existing key throws an error.
Best wishes
Julian
On 27/02/14 14:00, Dan Du wrote:
> Hi,
>
> To me it sounds like what I am expecting, from a R base point of view.
>
> x<-1:5
> names(x)<-letters[1:5]
> i<-'f'
&
Hi,
In the current bioc-stable and bioc-devel, a 'Seqinfo' object can be
indexed successfully with any character key, even it is non-existing:
#+BEGIN_SRC R
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg19)
si = seqinfo(BSgenome.Hsapiens.UCSC.hg19)
ind2 = "999"
ind2 %in% seq
Hi Sean,
You can have a look at the 'bam2R' function from the 'deepSNV' package.
This will extract the base/insertion/deletion counts, base call
qualities, and other metrics strand-specific from a BAM file.
Best wishes
Julian
On 13/02/14 17:09, Sean Davis wrote:
Hi, Martin.
How difficult
s
Julian
On 02/06/2014 01:58 PM, Michael Lawrence wrote:
Hi Julian,
Thanks for this one. It was a bug in Rsamtools, now fixed in devel, version
1.15.27. I'll leave it to Martin/Val to OK it and push to release.
Michael
On Thu, Feb 6, 2014 at 1:46 AM, Julian Gehring wrote:
Hi Michael,
Great, thanks for fixing this.
On 02/05/2014 08:38 PM, Michael Lawrence wrote:
Thanks, fixed in 1.9.35/1.8.11.
On Wed, Feb 5, 2014 at 1:21 AM, Julian Gehring wrote:
Hi,
I'm not sure whether this is related to the other bug. Anyway, 'writeVcf'
fails if the sample name
quot;) ## works
readVcf("out.vcf", "hg19") ## fails
#+END_SRC
Error in `rownames<-`(`*tmp*`, value = c("chr1", "chr2")) :
invalid rownames length
Best wishes
Julian
On 02/05/2014 08:38 PM, Michael Lawrence wrote:
Thanks, fixed in 1.9.35/1.8.11.
On We
Hi,
I'm not sure whether this is related to the other bug. Anyway,
'writeVcf' fails if the sample names of a 'VRanges' object are not
sorted in ascending order (in the latest bioc-devel):
#+BEGIN_SRC R
library(VariantAnnotation)
vr = VRanges(1:2, IRanges(100:101, 200:201),
ref = c
Hi,
I just stumbled over the fact that 'writeVcf' for a 'VRanges' fails if
'sampleNames' is a factor with unused levels. Here a small example:
#+BEGIN_SRC R
library(VariantAnnotation)
example(VRanges)
writeVcf(vr, "out.vcf") ## works
f = sampleNames(vr)
f ## levels: a, b
levels(f) = c("a",
Hi,
while ggbio work well for 'GRanges' objects, it is not able to deal with
objects inheriting from a 'GRanges', e.g. a 'VRanges' object:
library(ggbio)
library(GenomicRanges)
library(VariantAnnotation)
gr = GRanges("1", IRanges(1, 10))
vr = as(gr, "VRanges")
autoplot(gr) ## works
autoplot(
Hi Dan,
This looks impressive! Will this also work for experimental data
packages which are split in two parts in the bioc SVN, separating the
external data from the actual package?
Best wishes
Julian
On 01/29/2014 09:32 PM, Dan Tenenbaum wrote:
Hi all,
We've made available a bridge betw
Hi,
R-2.13 introduced the byte code compiler package 'compiler' [1], which
can be used to precompile the R code of a package at installation time
(using the ByteCompile field in the Description file or '--byte-compile'
with R CMD INSTALL). I have been using this lately with my own
packages,
Hi,
With the convenience that seqnamesStyles offers now, having to specify
the chromosome name notation manually would feel like a step back. In
terms of subsetting genomic ranges, I normally think of four major
groups of interest:
- Toplevel/standard: 1,..22,X,Y,MT
- Autosomes: 1,..,22
- A
Hi Michael,
I would second your request. In a package I'll submitting soon, I have
a work-around for this by defining a set of functions like
'hsAutosomes', 'hsAllosomes' etc. that return the respective set of
human chromosome names. Perhaps on could incorporate this in the
'seqinfo' class,
ue for REF and each ALT.
Thanks for reporting this.
Valerie
On 12/09/2013 12:20 PM, Valerie Obenchain wrote:
Hi Julian,
I'm looking into this. It's likely that the chr7 file has an invalid
header for the AD variable (which should be appropriately handled by
readVcf()). I'll let y
Hi,
I tried to import example VCFs from 'VariantAnnotation' and convert it
to a 'VRanges' object. While this works fine for the 'chr22.vcf.gz', it
fails for the 'chr7-sub.vcf.gz' VCF:
#+BEGIN_SRC R
library(VariantAnnotation)
f = system.file("extdata", "chr7-sub.vcf.gz", package =
"VariantA
Hi,
Some of the chromosomes out in the world are fairly large (e.g. wheat
chr 3B with > 995 Mbp [1]). Currently, the 'seqlengths' of the
reference sequence are stored as 'integers' which do not allow to store
lengths of this size. Are there any plans of switching to 'doubles' or
64-bit inte
ow are you using Biostrings in this case?
On Mon, Nov 4, 2013 at 1:12 AM, Julian Gehring mailto:julian.gehr...@embl.de>> wrote:
Hi,
Would it be reasonable to (optionally) allow storing the reference
and alternative alleles in the 'VRanges' class as a 'DNAStringSet&
Hi,
Would it be reasonable to (optionally) allow storing the reference and
alternative alleles in the 'VRanges' class as a 'DNAStringSet'?
Currently, 'character' and 'Rle' are possible. Having a 'DNAStringSet'
would make it more consistent with the rest of the 'VariantAnnotation'
framework a
Hi Elsa,
You can avoid this problem by using a 'GenomicRangesList' instead of a
'GRangesList'.
Best wishes
Julian
Second, I have to say that I just made a commit in the released version,
bumped from 1.0.0 to 1.0.1 in order to fix an important bug.
I was storing GRanges object into a GRanges
Hi Dan,
How does this behave in a competing situation when both a html and pdf
file with the same name are present? Will only be one of them linked or
both?
Best wishes
Julian
On 03/29/2013 11:16 PM, Dan Tenenbaum wrote:
Hi all,
I wanted to announce a small new feature of the Bioconducto
Hi,
What is the consensus on updating data in experiment data and annotation
packages?
The bioc website [1] does not state any differences between the two
package types in terms of updating their content. From the bioc core, I
have the information that (a) experimental data packages should
Hi,
It seems the issue has been resolved with the latest bioc build.
Best wishes
Julian
On 09/15/2013 04:01 PM, Julian Gehring wrote:
Hi,
calling 'head' or 'tail' on a 'RangedData' objects fail with the lastest
builds (R: 2013-09-14 r63932, IRanges: 1.19.35
Hi,
calling 'head' or 'tail' on a 'RangedData' objects fail with the lastest
builds (R: 2013-09-14 r63932, IRanges: 1.19.35). The cause seems to be
that there is no 'extractROWS' method that can be found for the
signature 'RangedData'. As an example, see:
'''
library(IRanges)
## generate
GRanges.
Michael
On Tue, Sep 3, 2013 at 2:39 AM, Julian Gehring wrote:
Hi Michael,
The use case is storing experimental metadata togther with a GRanges
object that does not fit the tabular structure of a GRange. And at a later
stage, storing multiple of these annotated GRanges objects togeth
Hi Michael,
The use case is storing experimental metadata togther with a GRanges
object that does not fit the tabular structure of a GRange. And at a
later stage, storing multiple of these annotated GRanges objects
together as a list/GRangesList.
Best wishes
Julian
This second case is ex
Hi,
It seems to me that constructing a 'GRangesList' object containing
'GRanges' with metadata does not keep the metadata. As an example:
* Example 1
library(GenomicRanges)
gr = GRanges()
metadata(gr) = list(a = "1")
metadata(gr) ## the metadata was stored
grl = GRangesList(gr, gr) ## put it
Hi,
Using the 'autoplot' method for plotting a region of 'TranscriptDb'
object seems to hang for certain regions, taking up lots of memory and
finishing only after several minutes:
library(ggbio)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(biovizBase)
data(genesymbol)
## this exampl
Hi,
Unlisting does not work on a list with a 'DNAString' as a element, the
resulting object is still a list. Is this behavior intentional? Here
an example that reproduces the issue in both the latest
R-devel/bioc-devel and R-2.15.3/bioc-stable.
library(Biostrings)
d = DNAString("TTGAA
Hi,
When I want to compare two aligned sequences of the same length and find
the mismatching positions, 'compareStrings' from the 'Biostrings'
package seems to be the best choice. However, it does take into account
any ambiguous matches (as matching any base to 'N'), as it can be found
with
is case?
Thanks,
Valerie
On 02/26/13 09:50, Julian Gehring wrote:
Hi,
I tried to use the latest devel version of 'readVcf' to import a VCF
file with information from the ensembl VEP
(http://www.ensembl.org/info/docs/variation/vep/index.html).
For a VCF entry with CSQ information
Hi,
'VEPParam' allows to set the parameters for the ensembl VEP perl script,
and the documentation of 'ensemblVEP' specifies:
"""
- fork: ‘logical’, default FALSE; enable forking
"""
However, looking at the VEP documentation
(http://www.ensembl.org/info/docs/variation/vep/vep_script.html#f
version-41
"INFO additional information: (String, no white-space, semi-colons, or
equals-signs permitted;"
So that equals-sign in your INFO isn't allowed
HTH
Richard
On 26/02/2013 17:50, Julian Gehring wrote:
Hi,
I tried to use the latest devel version of 'readVcf'
Hi,
I tried to use the latest devel version of 'readVcf' to import a VCF
file with information from the ensembl VEP
(http://www.ensembl.org/info/docs/variation/vep/index.html).
For a VCF entry with CSQ information like
""
1 887899 . A G . .
NS=1;CSQ=G|ENSG0188976|ENST0327044|Transcr
Hi,
when constructing a 'GRanges' object with a metadata column named 'c',
the construction fails with
"""
Error in .getClassFromCache(Class, where) :
class should be either a character-string name or a class definition
"""
both in R-2.15.2 and the latest R-devel (2013-02-21 r62017).
Here
Hi,
Since the attached file didn't make it all the way through to the
mailing list, you can find it at
http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/0001-Example-patch-for-naming-samples-in-BAMQA.patch.
Best wishes
Julian
On 02/12/2013 03:23 PM, Julian Gehring wrote:
Hi,
In t
Hi,
In the QA report of the 'ShortRead' package, a short sequential integer
labeling for referencing the samples/files throughout the report is
created by default. Would it be reasonable/possible to allow for other
optional names to label the samples to make the results of the report
easier
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