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 res
Hello,
On support.bioconductor.org, we've seen a lot of instances of people
using the answer box when they should be adding a comment on an existing
answer. I don't necessarily blame uses, since the "Add your answer" text
box is far more obvious than the "add comment" button on an existing
an
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, bump
From base, according to my R console:
> subset
standardGeneric for "subset" defined from package "base"
function (x, ...)
standardGeneric("subset")
Methods may be defined for arguments: x
Use showMethods("subset") for currently available ones.
On 07/29/2015 10:40 AM, Steve Lianoglou wrote:
t.
Best,
Matt
On Mon, Jul 6, 2015 at 5:42 PM, Ryan C. Thompson <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.cha
o ifelse 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
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
Ivana
Dne 2015-06-16 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)
prepareSPI
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 Bioconduct
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
signalli
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
t
tq assuming it can read from connections
> rather than just files, but I have not tested it to be sure.
>
> On Wed, Apr 22, 2015 at 1:16 PM, Ryan C. Thompson
> mailto:r...@thompsonclan.org>> wrote:
>
> That's not ideal because it's duplicating storag
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: Append/co
Hello,
Often when sequence data is delivered to me, I receive each sample in
several input files. Generally I want to get them into a single file
ASAP, and the filterFastq step would be a convenient place to do it. Is
there any possibility to add some way to append to an output file, or
maybe
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 setti
I'd just like to chime in that regardless of what approach is chosen, I
definitely would appreciate a way to get the plot data without actually
making the plot. I often end up reimplementing plots in ggplot so that
I can easily customize some aspect of them, so in such cases I need a
way to jus
olving via a
pull request? Would social coding increase external contributions to
the infrastructure?
On Mon, Oct 6, 2014 at 5:13 PM, Ryan C. Thompson mailto:r...@thompsonclan.org>> wrote:
Hi,
I've just noticed that DataFrame doesn't have a "dropleve
Hi,
I've just noticed that DataFrame doesn't have a "droplevels" method, but
"data.frame" does. In fact, "droplevels.data.frame" seems to work just
fine on DataFrame objects. Could this be added?
-Ryan
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
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.
This
ads function should be required to
only take one argument, or else the method of passing through
additional arguments to it should 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 f
fix,
use.names=use.names,
ignore.strand=ignore.strand))
ov <- findOverlaps(features, reads, type=type,
ignore.strand=ignore.strand,
maxgap=maxgap, minoverlap=minoverlap)
if (inter.feature) {
## Remove reads that overlap multiple features.
reads_to_keep <- which(countSubjectHits(ov) == 1L)
ov
Hello,
I think I may have found a bug in the code for aveLogCPM.default in the
edgeR package. Near the end of the function, the variable
"prior.count.scale" is conditionally assigned to, and never subsequently
used. I assume this is a typo and the variable name is supposed to be
"prior.count.
M PDT, 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
Hello,
I recently found myself in want of a nearest method that handles
GRangesList objects. Is there any plan to add one? I just want to define
"nearest" for elements of a GRangesList by the shortest distance between
any query range and any subject range. Obviously I can do this by
unlisting
04/30/2014 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 c
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 c
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
Hello,
I have discovered a bug in the cdfDuplicates function in the les
package. This function is used indirectly by the GSRI package, and I was
attempting to use this package when I encountered an error. The error
appears to occur because both rle and table are used to deduplicate a
(sorted)
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’
ob
Indeed, loading rJava and calling .jinit() also triggers the bug. I
have updated my script (same URL as before) to demonstrate this. I run
the bad code before and after calling .jinit(), and it only crashes the
second time.
On Mon 16 Dec 2013 02:30:34 PM PST, Simon Urbanek wrote:
On Dec 16, 2
By the way, here is my sessionInfo after a successful run of the bug
script (without loading xlsxjars):
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UT
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
Actually, scratch that. I just tried running subread-buildindex on a
file with only the 20-ish chromosome sequences, and it didn't give the
message about 5 sections, but it still crashed with "Killed" and
exit code 137.
On Tue 26 Nov 2013 05:01:48 PM PST, Ryan C. Thompso
Hello,
I'm trying to test out subjunc for mapping my RNA-seq data to the
cynomolgus monkey genome, but when I try to build the index with
subread-buildindex, I get the error:
"There are too many sections in the chromosome data files (more than
5 sections)."
and then after "Building the
Just a note: the foreach package has solved this by providing a
"nesting" operator, which effectively converts multiple nested foreach
loops into one big one:
http://cran.r-project.org/web/packages/foreach/vignettes/nested.pdf
On Thu 14 Nov 2013 09:24:29 AM PST, Michael Lawrence wrote:
I like
atics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth
On Thu, 29 Aug 2013, Ryan C. Thompson wrote:
Hi Gordon,
I am currently working on some code that would benefit from having
direct access to the co
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 Gordon,
I'm implementing the "voom-by-group" procedure that you suggested
previously, and I'm running into a small snag: when I call voom several
times to get several EList objects, I then need to cbind them together.
However, the design and lib.size components of the ELists are not
merged
With such a huge difference, I would wonder if the "c" method for
GRanges objects is doing N-1 pairwise merges instead of a single N-way
merge.
On Mon 07 Jan 2013 09:08:28 AM PST, Michael Lawrence wrote:
Would be interesting to do some profiling. Could be the merging of the
sequence info, or t
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))".
An
Dear Gordon,
On 12/10/2012 11:06 PM, Gordon K Smyth wrote:
I don't see a proposal below, only a question.
Yes, I ended up not really proposing anything because I realized that I
didn't really have anything that improves on linear modeling. But see
below for what I was trying to get at.
Wha
Dear Gordon,
After a bit of pen-and-paper work, I see what you mean about additive
models. I constructed a simple 2x2 additive model (i.e. "~a+b" where a
and b each have 2 levels) and tried to solve for all 4 groups, and found
that it was impossible. The best that can be done is solving for tw
Hi Gordon and list,
I've been thinking about how to make it easier to specify what
hypotheses one wants to test in microarray or RNA-seq differential
expression data sets, and I think one of the major stumbling blocks that
confuses people is the way in which design matrices must have one
coef
Hi all,
I'm working with an RNA-seq dataset where every biological sample has
two technical replicates. Is important for me to merge the technical
replicates so that my count matrix has exactly one column per biological
sample, or is it ok to leave them separate? My worry would be that
leavin
Perfect, that's just what I wanted for Fastq files. Is there no R
facility for reading unindexed bam?
On Tue 04 Dec 2012 02:47:56 PM PST, Martin Morgan wrote:
On 12/04/2012 01:27 PM, Ryan C. Thompson wrote:
Hi all,
I'm currently experimenting with using quip
(https://github.com/dc
ction that is to mapply as mclapply is to
lapply. I plan to implement a param-generic version called bpmapply,
which may become the backend for bpvectorize.
On Tue 04 Dec 2012 01:15:24 PM PST, Michael Lawrence wrote:
On Tue, Dec 4, 2012 at 12:47 PM, Ryan C. Thompson
mailto:r...@thompsonclan.o
Hi all,
I'm currently experimenting with using quip
(https://github.com/dcjones/quip#readme) to save disk space when storing
FASTQ and BAM files. One thing that would be nice is to read
quip-compressed FASTQ or BAM files directly into R. Obviously direct
support for reading quip compression w
One issue that I see is that for some kinds of parallel backends, there
may not be any way for "bpworkers" to return something meaningful. For
example, a backend that submits jobs to a large cluster may not know
exactly how many nodes are in the cluster, and in any case returning the
total numb
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
In my work, I've developed a few useful functions relating to edgeR and
DESeq. First, I wrote a version of glmQLFTest that does not throw errors
on zero-count genes. See the comment for details on what exactly it does:
## This version of glmQLFTest excludes genes with zero counts in all
## samp
On 11/17/2012 08:38 PM, Michael Lawrence wrote:
You can use mclapply via parLapply using the fork backend.
Oh, well, that's new to me. I guess that was added when multicore and
snow were merged into the parallel package? If that's so, then parLapply
is perfectly fine to use. However, I will not
Actually, my previous post had a small bug in it: it would throw an
error when printing a zero-column data frame. The following code fixes this:
print.data.frame <- function(df) {
if (ncol(df) > 0 && require("IRanges")) {
prev.max.print <- getOption("max.print")
on.exit(options(max.pri
Hi all,
I noticed that DataFrame objects have a much faster and more practical
printing format than base R's data.frame class. So I wrote a replacement
for "print.data.frame" that prints data.frames in the same style as
DataFrames. Just stick it in your ~/.Rprofile and your data.frames will
m
On 11/17/2012 02:39 AM, Ramon Diaz-Uriarte wrote:
In addition to Steve's comment, is it really a good thing that "all code
stays the same."? I mean, multiple machines vs. multiple cores are,
often, _very_ different things: for instance, shared vs. distributed
memory, communication overhead diff
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
you have to do is register a different
backend, which is one line of code to load the new backend and a second
one to register it, and the rest of your code stays the same.
On Fri 16 Nov 2012 03:24:56 PM PST, Michael Lawrence wrote:
On Fri, Nov 16, 2012 at 11:44 AM, Ryan C. Thompson
mailto:r
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. Th
27;m not sure I understand the appeal of foreach. Why not do this
within the functional paradigm, i.e, parLapply?
Michael
On Fri, Nov 16, 2012 at 9:41 AM, Ryan C. Thompson
mailto:r...@thompsonclan.org>> wrote:
You could write a %dopar% backend for the foreach package, which
would
You could write a %dopar% backend for the foreach package, which would
allow any code using foreach (or plyr which uses foreach) to parallelize
using your code.
On a related note, it might be nice to add Bioconductor-compatible
versions of foreach and the plyr functions to BiocParallel if they
You can probably parallelize the findOverlaps function, but you'd have
to write the code yourself, and that code would be mostly bookkeeping
code to get the indices right. Maybe there's a case for adding a
parallelized findOverlaps function to BiocParallel?
You can't parallelize the disjoin op
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 pv
Here are two alternative implementations of pvec. pvec2 is just a simple
rewrite of pvec to use mclapply. pvec3 then extends pvec2 to accept a
specified chunk size or a specified number of chunks. If the number of
chunks exceeds the number of cores, then multiple chunks will get run
sequentiall
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