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
This was a consideration. I guess I've never got much use out of them being
DNAStringSets, so I just went with the simple character vectors. It makes
sense to support DNAStringSet. I could imagine someone e.g. wanting to
represent mutations at the protein-level, and structural variants will
Actually, the check that I proposed is only supposed to check for usage
of user-defined variables, not variables from packages. Truthfully,
though, I guess I'm not the right person to work on this, since in
practice I use forked processes for the vast majority of my inside-R
parallelization,
Hi Michael,
Sure, I'll try to dig into it and construct a patch that adds this feature.
I stumbled upon this after converting data between the 'VCF' and
'VRanges' class. The primary use case I had in mind is having a more
efficient storing and processing for short InDels, or defining
Weird, I guess it needs to be logged in or something. I don't know if the
issue is that its in a non-master branch or waht. The repo is fully public
and the forCRAN_0.3.5 in branch definitely exists on github.
I started chrome (where I'm not logged into github) and got the same 404
error but
The code that I wrote intentionally avoids checking for package variables,
since I consider that a separate problem. Package variables can be provided
to the child by leading the package, whereas user-defined variables must be
serialized in the parent and sent to the child.
I think I could fairly
Ryan,
I agree that in some sense it is a different problem, but my point is with
a different approach we can easily answer both. The code I posted returns a
named character vector of symbol names with package name being the name.
This makes it a trivial lookup to determine both a) what symbols
On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Tim Triche, Jr. tim.tri...@gmail.com
To: bioc-devel@r-project.org
Sent: Monday, November 4, 2013 12:25:19 PM
Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave on
On 11/4/13, 11:05 AM, Gabriel Becker wrote:
As a side note, I'm not sure that existence of a symbol is sufficient (it
certainly is necessary). What about situations where the symbol exists but
is stale compared to the value in the parent? Are we sure that can never
happen?
I think this is a
Le 03/11/2013 22:45, Michael Kane a écrit :
I'd like to echo Whit's sentiment and hopefully warm up this thread.
C++11's new features and functionality give R users low-level tools (like
threads, mutexes, futures, date-time, and atomic types) that work across
platforms and wouldn't require other
Dear all,
Is there a reason, why there is no +-operator for aes (i.e. uneval) objects (as
there is for themes and gg objects)? I had a couple of cases where such an
operator would be useful, for instance to combine the result of aes and
aes_string in functions. Any flaws with the following
This seems like a conversation to have with the package's maintainer
(Hadley), as suggested by the posting guide:
http://www.r-project.org/posting-guide.html
If the question relates to a contributed package , e.g., one downloaded
from CRAN, try contacting the package maintainer first.
and
I'm using R in a regulated environment and one of the requirements is to
be able to trace how a result is arrived at. I would like to be able to
determine which files are opened in read or write mode by an R session,
for example when a program uses source, sink, file, open, read.table,
I am not sure R can do what you want (others may), but have a look at
?history
for R's history mechanism, which keeps a record of all commands that
you have entered and so might satisfy your needs.
Note that there are various 3rd party GUI's/IDE's (e.g. RStudio) that
might be more to your
If you have the code in a parseable form then CodeDepends will try to do
this:
library(CodeDepends)
code
[1] w = rnorm(10); t = read.csv('mycsv.csv'); lm(y~x, data = t)
scr = readScript(dummy, type = R, txt = code)
inp = getInputs(scr)
length(inp)
[1] 3
inp[[2]]@files
[1] mycsv.csv
The
Most operating systems have tools which allow you to audit the resources
used by a running process, for example the 'lsof' (list open files) command
on Unix and MacOS X. Or, for more complex dynamic tracing, the DTrace
framework again on MacOS X or BSD Unix.
Not sure what the Windows equivalent
On 4 November 2013 at 14:31, Murray Stokely wrote:
| Most operating systems have tools which allow you to audit the resources
| used by a running process, for example the 'lsof' (list open files) command
| on Unix and MacOS X. Or, for more complex dynamic tracing, the DTrace
| framework again on
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