Hi Yue,
On Tue, Feb 26, 2013 at 7:42 PM, Yue Li wrote:
> Dear developer community,
>
> There seems to be an error in the nightly build of my package `RIPSeeker'
> (0.99.8) on the Mac OS X Leopard (10.5.8) / i386 (petty) (message pasted
> below).
>
> The error occurs in the Vignette demo. Howeve
Dear developer community,
There seems to be an error in the nightly build of my package `RIPSeeker'
(0.99.8) on the Mac OS X Leopard (10.5.8) / i386 (petty) (message pasted below).
The error occurs in the Vignette demo. However, I have not updated my package
and cannot figure out why that occur
Bioc-develers,
Wanted to mention a change to R svn revision 62015 arising from
https://stat.ethz.ch/pipermail/r-devel/2013-January/065700.html
when the first argument, x, is a class. Previously, the behaviour was like
ind <- split(seq_along(f), f)
lapply(ind, function(i) x[i])
but
Yep, that works. Thanks!
Want a patch? (Which you essentially just wrote?) ;-)
Much obliged,
--t
On Tue, Feb 26, 2013 at 2:19 PM, Hervé Pagès wrote:
> Hi Tim,
>
>
> On 02/26/2013 02:01 PM, Tim Triche, Jr. wrote:
>
>> It seems like the best way to write an email around these parts is usi
Hi Tim,
On 02/26/2013 02:01 PM, Tim Triche, Jr. wrote:
It seems like the best way to write an email around these parts is using R
code, so here goes. I'm just wondering why a coercion that I define for
DataFrame -> data.frame doesn't automatically get used in practice.
library(Biobase)
librar
It seems like the best way to write an email around these parts is using R
code, so here goes. I'm just wondering why a coercion that I define for
DataFrame -> data.frame doesn't automatically get used in practice.
library(Biobase)
library(GEOquery)
library(GenomicRanges)
## download a dataset
On 2/26/2013 8:17 AM, Tengfei Yin wrote:
Hi Martin,
Sorry for the late update, actually, it's not a bug in VariantAnnotation, I
checked the files, it's the header problem, got it from some collaborators, they
are using their own scripts to combine vcf files, and use vcftools instead
solved the
Hi Julian,
Thanks for the bug report. I agree this situation should be handled. It
might be tomorrow before I get to this - I'll post back when it is done.
Valerie
On 02/26/2013 10:23 AM, Julian Gehring wrote:
Hi Richard,
That is true that is not according to the specs. However, the
'ensem
On Tue, Feb 26, 2013 at 1:23 PM, Julian Gehring wrote:
> Hi Richard,
>
> That is true that is not according to the specs. However, the 'ensemblVEP'
> package has the 'parseCSQToGRanges' method which extracts this kind of CSQ
> information from a 'VCF' object (as read in by 'readVcf') and fails at
Hi Richard,
That is true that is not according to the specs. However, the
'ensemblVEP' package has the 'parseCSQToGRanges' method which extracts
this kind of CSQ information from a 'VCF' object (as read in by
'readVcf') and fails at the prematurely ended entries. Perhaps having a
VCF reader
Hi Julian
I think your vcf file is off-spec. From the vcf spec at
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
"INFO additional information: (String, no white-space, semi-colons, or
equals-signs permitted;"
So that equals-sign in your INFO
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 Martin,
Sorry for the late update, actually, it's not a bug in VariantAnnotation, I
checked the files, it's the header problem, got it from some collaborators,
they are using their own scripts to combine vcf files, and use vcftools
instead solved the problem.
Thanks again
Tengfei
On Tue, Fe
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