Would it make sense for an OrganismDb object to have an associated
BSgenome? This association is implicit anyway. Or do we need an even
broader umbrella object? This would make some things easier. For example,
predictCoding(variants, Homo.sapiens). Just nice to have everything in one
bundle. Also,
Let's say I have a vector of gene IDs where some are NA, and are some are
repeated, and I want to map them to gene symbols, where I get NAs for the
NA IDs or IDs without a symbol. What is the best way to do this?
I tried select() but it gave me a table with unique entries; not very
convenient. It
hi Michael,
this souns like if you had a list of variants where you have annotated
their Entrez Gene IDs, which sometimes are NA because those variance do
not overlap any gene and sometimes are repeated Entrez Gene IDs when two
or more of those variants overlap the same gene :)
at least is
Wow, VariantFiltering is awesome. It's impressive how it integrates all of
the annotation resources so seamlessly. And the shiny app looks very
useful. This should be a model package for where we want to bring
Bioconductor.
You should look into using VRanges instead of GRanges for the return
hi, thanks of the compliments to the package, i'm happy to hear you
liked it! i must acknowledge that part of the design of the package is
the result of conversations i had with Martin, Marc and specially
Valerie during the review process.
i only got to know about VRanges once the package was
I can't install this DESEq2 on the RHEL 5.5 server:
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums
checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD unavailable via
R-
supplied
hi Jarod,
What version of Rcpp and RcppArmadillo is installed?
Mike
On Wed, Jun 18, 2014 at 11:35 AM, jarod...@libero.it jarod...@libero.it wrote:
I can't install this DESEq2 on the RHEL 5.5 server:
* installing *source* package ‘RcppArmadillo’ ...
** package
Hi Michael,
On 06/18/2014 06:03 AM, Michael Lawrence wrote:
Let's say I have a vector of gene IDs where some are NA, and are some are
repeated, and I want to map them to gene symbols, where I get NAs for the
NA IDs or IDs without a symbol. What is the best way to do this?
I tried select() but
Thanks for your help
I have the 2.0 when i try to install 3.8 I have the error on version of gcc
on Rhel5.5
Messaggio originale
Da: michaelisaiahl...@gmail.com
Data: 18/06/2014 17.44
A: jarod...@libero.itjarod...@libero.it
Cc: bioc-devel@r-project.orgbioc-devel@r-project.org
Ogg: Re:
That is a good start. But for convenience, I would favor something that
just returns the vector corresponding to column rather than a data.frame.
Thanks,
Michael
On Wed, Jun 18, 2014 at 10:11 AM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Michael,
On 06/18/2014 06:03 AM, Michael Lawrence
Seconded, this would be so useful. I still use mget() for heavens sake.
Meanwhile I'm going to try VariantFiltering. Thanks for starting this
conversation Michael.
--t
On Jun 18, 2014, at 11:18 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
That is a good start. But for
are you installing with:
biocLite(DESeq2)
hmm these don't look like Rcpp* version numbers. What do you get with
library(Rcpp)
library(RcppArmadillo)
sessionInfo()
On Wed, Jun 18, 2014 at 1:13 PM, jarod...@libero.it jarod...@libero.it wrote:
Thanks for your help
I have the 2.0 when i try to
Hi Peter,
Just added support for dbSNP seqlevels style for Human (in
GenomeInfoDb 1.1.9, will become available tomorrow):
library(SNPlocs.Hsapiens.dbSNP.20120608)
myrsids - c(rs2639606, rs75264089, rs73396229, rs55871206,
rs10932221, rs56219727, rs73709730, rs55838886,
On 06/18/2014 05:26 AM, Michael Lawrence wrote:
Would it make sense for an OrganismDb object to have an associated
BSgenome? This association is implicit anyway. Or do we need an even
broader umbrella object? This would make some things easier. For example,
predictCoding(variants, Homo.sapiens).
Sounds nice but we have to be careful. We may need a parameter:
Homo.sapiens(hg19) ... because
broad adoption of new builds may take considerable time.
On Wed, Jun 18, 2014 at 6:13 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 06/18/2014 05:26 AM, Michael Lawrence wrote:
Would it make sense
Multiple inheritance might work. May be a good time to think about an
abstract sequence source, i.e., anything that supports getSeq(). Right
now, we use ANY for that, which is not ideal. Same for transcript source.
We've already implemented the TxDb API directly on top of biomaRt.
On Wed, Jun
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