Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that converts a vector of comma-separated character
strings to a DNAStringSetList. I'd like to use this code in a package
I'm working on. Would it make sense to export this from Biostrings? If
not,
why not just use
VariantAnnotation:::.toDNAStringSetList()
?
On Fri, Apr 19, 2013 at 11:55 AM, Stephanie M. Gogarten
sdmor...@u.washington.edu wrote:
Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that converts a vector of comma-separated
Hi Stephanie,
On 04/19/2013 11:55 AM, Stephanie M. Gogarten wrote:
Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that converts a vector of comma-separated character
strings to a DNAStringSetList. I'd like to use this code in a package
I'm working on.
Greetings,
I'm kicking tires on the new DESeq2 package -- very nicely done, btw,
thanks!.
I have a quick question about the use of the variance and rlog
transformations.
It seems that both functions prefer to receive a DESeqDataSet with a design
set to formula(~ 1). I say prefer because while
Thanks, Herve!
To answer Tim's question (though it has become irrelevant after Herve's
solution): because I'd rather not add VariantAnnotation to my dependency
tree for only a couple of lines of code. It also seemed like the sort
of thing that should be possible with a DNAStringSetList
On 13-04-19 8:41 AM, Therneau, Terry M., Ph.D. wrote:
I went through the same problem and discovery process 2 years ago with the
survival package. With pspline() terms the return object from coxph includes
a simple 6 line function for enhanced printout, which by default carried along
On 18.04.2013 18:05, José Matos wrote:
On Thursday 18 April 2013 17:38:06 Thomas Petzoldt wrote:
Dear R developers,
I've got an information from Prof. Ripley regarding a bug found
with AdressSanitizer in one of our packages. It is now fixed, thank
you for this information.
Now, I would like
Duncan,
I stand by all my comments. Well behaved function -- those that look
only at their input arguments -- do just fine with a simple env.
Now as to formulas --- the part of R that has most aggressively messed
with normal evaluation rules. It is quite possible that there is/was no
other way
On 19/04/2013 18:22, Thomas Petzoldt wrote:
On 18.04.2013 18:05, José Matos wrote:
On Thursday 18 April 2013 17:38:06 Thomas Petzoldt wrote:
Dear R developers,
I've got an information from Prof. Ripley regarding a bug found
with AdressSanitizer in one of our packages. It is now fixed, thank
hmm. I have tested a bit more, and found this perhaps more difficult
solve situation. even though I delete x, since x is part of the output
of the formula, the size of the object is twice as much as it should be:
test - function(x){
x - rnorm(100)
out - list(x=x)
rm(x)
out$f -
On Apr 19, 2013, at 2:19 PM, Prof Brian Ripley wrote:
On 19/04/2013 18:22, Thomas Petzoldt wrote:
On 18.04.2013 18:05, José Matos wrote:
On Thursday 18 April 2013 17:38:06 Thomas Petzoldt wrote:
Dear R developers,
I've got an information from Prof. Ripley regarding a bug found
with
Having finally found some free time, I was going to use it to update a
bunch of R packages from 2.15 to 3.0.
I am running Windows 7, 64-bit professional. This is on a brand-new
laptop using vanilla settings when installing the operating system.
Problem 1: I installed R3.0 to the default
On 13-04-19 5:37 PM, Kevin Coombes wrote:
Having finally found some free time, I was going to use it to update a
bunch of R packages from 2.15 to 3.0.
I am running Windows 7, 64-bit professional. This is on a brand-new
laptop using vanilla settings when installing the operating system.
On Fri, Apr 19, 2013 at 8:47 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 13-04-19 5:37 PM, Kevin Coombes wrote:
Having finally found some free time, I was going to use it to update a
bunch of R packages from 2.15 to 3.0.
I am running Windows 7, 64-bit professional. This is on a
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