Hello,
I was recently bitten by an unexpected behavior in the sraConvert
function from the SRAdb package. I wanted to fetch the other SRA IDs
associated with the SRX numbers of 32 samples, and I used the sraConvert
function to do so. However, I did not realized that sraConvert returns
the
Konsole output Hello,
I was recently setting up the latest version of R Bioc on a system,
installing all packages from scratch, and I ran into an error while
installing bumphunter. It failed to install because it couldn't load the
digest package. After installing this package manually,
From base, according to my R console:
subset
standardGeneric for subset defined from package base
function (x, ...)
standardGeneric(subset)
environment: 0x4eb60c8
Methods may be defined for arguments: x
Use showMethods(subset) for currently available ones.
On 07/29/2015 10:40 AM, Steve
at 5:42 PM, Ryan C. Thompson r...@thompsonclan.org
mailto:r...@thompsonclan.org wrote:
I also discovered another apparent bug later in the same function.
The second to last line of makeVectorsAffyBatch is
vers - ifelse(!is.null(cdfname),
as.character(packageVersion(cdfname
Hello,
I just encountered a bug in frmaTools that makes it impossible to use on
certain array platforms. The following lines in makeVectorsAffyBatch
fail on an AffyBatch object on the hthgu133pluspm platform:
pms - pm(object)
pns - probeNames(object)
pmi - unlist(pmindex(object))
will have length zero and ifelse does NOT do lazy
evaluation.
On 07/06/2015 12:21 PM, Ryan C. Thompson wrote:
Hello,
I just encountered a bug in frmaTools that makes it impossible to use
on certain array platforms. The following lines in
makeVectorsAffyBatch fail on an AffyBatch object
Hello,
I was attempting to run SPIA through the graphite package and ran into
an odd error when running prepareSPIA on the human Reactome pathways.
You can reproduce the error simply and quickly by:
library(graphite)
prepareSPIA(pathways(hsapiens, reactome)[Insulin receptor
signalling
-06-16 21:17, Ryan C. Thompson napsal:
Hello,
I was attempting to run SPIA through the graphite package and ran into
an odd error when running prepareSPIA on the human Reactome pathways.
You can reproduce the error simply and quickly by:
library(graphite)
prepareSPIA(pathways(hsapiens, reactome
This is great to hear. I sometimes want to delve into the source code of
a package's internals, but doing so through the SVN web interface is
clunky. Being able to use Github's repo browsing functionality for Bioc
packages is great.
On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear
Hi all,
So, dplyr is a pretty cool thing, but it currently works with data.frame
and data.table, but not S4Vectors::DataFrame. I'd like to change that if
possible, and I assume that this would simply involve writing some
glue code. However, I'm not really sure where to start, and I expect
That's not ideal because it's duplicating storage unnecessarily.
On 04/22/2015 04:07 AM, Aedin wrote:
This is one instance were a system or simple unix command is very easy
system('cat *.fastq all.fastq')
---
On Apr 22, 2015, at 6:00, bioc-devel-requ...@r-project.org wrote:
Re:
I thought CRAN packages weren't allowed to depend on Bioconductor
packages for exactly this reason.
On 03/02/2015 03:18 PM, Laurent Gatto wrote:
Dear all,
I had never realised that CRAN packages that depended on Bioc packages
could actually not be installed with install.packages without
? Would social coding increase external contributions to
the infrastructure?
On Mon, Oct 6, 2014 at 5:13 PM, Ryan C. Thompson r...@thompsonclan.org
mailto:r...@thompsonclan.org wrote:
Hi,
I've just noticed that DataFrame doesn't have a droplevels
method, but data.frame does. In fact
Hi all,
Just to throw in a suggestion here, I know that many people use a tool
like git-svn in this kind of situation. They want the ability to make
multiple small commits in order to save their progress, but they don't
want those commits visible until they are ready to push all at once.
) %in% reads_to_keep]
}
countQueryHits(ov)
}
To count the overlaps of 5' and 3' ends:
summarizeOverlaps(reads, features, chipseq, fix=start, width=1)
summarizeOverlaps(reads, features, chipseq, fix=end, width=1)
Valerie
On 04/30/2014 02:41 PM, Ryan C. Thompson wrote:
No, I forgot to attach
be documented.
-Ryan
On Tue 05 Aug 2014 05:12:41 PM PDT, Ryan C. Thompson wrote:
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote
, Hervé Pagès wrote:
Hi Ryan,
On 05/22/2014 03:38 PM, Ryan C. Thompson wrote:
Hello,
I recently found myself in want of a nearest method that handles
GRangesList objects. Is there any plan to add one?
Not that I know of. I guess most of the times it's probably good enough
to call range() on both
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward writing a custom
function to pass as the mode parameter. I have now written the custom
modes that I require for counting my ChIP-Seq reads, and I figured I
would
/2014 01:06 PM, Ryan C. Thompson wrote:
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward writing a custom
function to pass as the mode parameter. I have now written the custom
modes that I require for counting my ChIP-Seq
Hi all,
I noticed that the seqinfo works on BamFile objects, but not on
BamFileList objects. For BamFileList, it does not throw an error, but
rather uses the inherited method for List, which does not return a
useful result for BamFileList. I suggest the following implementation of
a useful
I would prefer the droplevels method for SummarizedExperiment, since
this is consistent with the use of droplevels on data.frame objects.
On Wed 12 Mar 2014 03:02:37 PM PDT, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
Hello,
I have found an issue where having the xlsxjars package loaded kills the
entire R session with a segfault when edgeR::estimateDisp is called on
my dataset. The issue seems to be specific to my data, since a random
integer matrix of identical dimension does not trigger the bug. Other
Hi Gordon,
I am currently working on some code that would benefit from having
direct access to the code in edgeR::glmLRT that handles reparametrizing
the design matrix so that the N linearly independent components of the
specified contrasts are represented in the first N columns of the design
Hi Dario Strbenac,
Are you asking if you can rewrite your code to work faster, or are you
asking if the BioC devs need to improve the code to be faster? As a
first test, I would try a few alternatives to see if they are
significantly faster. One would be unlist(GRangesList(blockRanges)).
On Tue 04 Dec 2012 11:31:59 AM PST, Michael Lawrence wrote:
The name pvec is not very intuitive. What about bpchunk? And since the
function passed to bpvectorize is already vectorized, maybe bpvectorize
should be bparallelize? I know everyone has different
intuitions/preferences when it comes to
In reply to:
On 11/16/2012 09:45 PM, Steve Lianoglou wrote:
But then you have the situation of multi-machines w/ multiple cores --
is this (2) or (3) here? How do you explicitly write code for that w/
foreach mojo? I guess the answer to that is that you let your grid
engine (or whatever your
To be more specific, instead of:
library(parallel)
cl - ... # Make a cluster
parLapply(cl, X, fun, ...)
you can do:
library(parallel)
library(doParallel)
library(plyr)
cl - ...
registerDoParallel(cl)
llply(X, fun, ..., .parallel=TRUE)
On Fri 16 Nov 2012 11:44:06 AM PST, Ryan C. Thompson wrote
I just submitted a pull request. I'll add tests shortly if I can figure
out how to write them.
On Wed 14 Nov 2012 03:50:36 PM PST, Martin Morgan wrote:
On 11/14/2012 03:43 PM, Ryan C. Thompson wrote:
Here are two alternative implementations of pvec. pvec2 is just a
simple rewrite
of pvec
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