for a CoMeth object containing multiple samples, i.e. MMM
is a matrix-like object with ncol = # of samples, MMU is matrix-like object
with ncol = # of samples, etc. Was anything like this ever implemented? My
reading of the previous thread was to use a DataFrame but the "matrix API",
Apologies for the bump, but is anyone able to help me on this? Or are these
questions more appropriate for the general Bioconductor mailing list rather
than Bioc-Devel?
Many thanks,
Pete
- Original Message -
Date: Mon, 10 Feb 2014 13:20:47 +1100
From: Peter Hickey
To: bioc-devel@r
tMethod('findOverlaps', c('Vector', 'SummarizedExperiment'))
Method Definition:
function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
"start", "end", "within", "equal"), select = c("all", "first"
Thanks for the explanation and the update, Martin.
Cheers,
Pete
- Original Message -
From: Martin Morgan
To: Peter Hickey , bioc-devel@r-project.org
Sent: Sat, 12 Apr 2014 06:45:46 +1000 (EST)
Subject: Re: [Bioc-devel] Restrictions on findOverlaps parameters with
SummarizedExperiment
UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] IRanges_1.22.7 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] stats4_3.1.0
-
reaks I get the error:
>> --
>> Error in Rle(values = callGeneric(runValue(e1)[which1],
>> runValue(e2)[which2]), :
>> error in evaluating the argument 'values' in selecting a method for
>> fu
memoise_0.2.1
RCurl_1.95-4.1
[7] stats4_3.1.0 stringr_0.6.2 tools_3.1.0whisker_0.3-2
------
On 28/05/2014, at 3:23 AM, Hervé Pagès wrote:
> Hi Peter,
>
> On 05/26/2014 04:37 PM, Peter Hickey wro
ans that these need to be renamed to use with most other
Bioconductor data sources.
Thanks,
Pete
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia
le infrastructure in GenomeInfoDb that may help.
>
>
> On Tue, Jun 17, 2014 at 8:17 PM, Peter Hickey wrote:
> Is there a reason why the seqnames of SNPlocs.Hsapiens.dbSNP.20120608 (and
> possibly the other SNPlocs.*) use the prefix "ch" instead of "chr"? E.g.
&g
5-4.3
[9] stats4_3.1.1 stringr_0.6.2tools_3.1.1 whisker_0.3-2
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
ix.
Thanks,Pete
- Original Message -From: Michael Lawrence
To: Peter Hickey Cc:
bioc-devel@r-project.orgSent: Tue, 26 Aug 2014 13:35:35 +1000 (EST)Subject: Re:
[Bioc-devel] Valid classes for extraColumnSlots
Hi Peter,
Some code would help here. I'm not sure what you mean by havi
t; the problem and fix things.
>
> Thanks,
> Michael
>
>
> On Tue, Aug 26, 2014 at 4:25 AM, Peter Hickey wrote:
> Hi Michael,
>
> Sorry for my misunderstanding. Here is some code describing the class
> https://github.com/PeteHaitch/GenomicTuples/blob/master/R/GTupl
>
>
> On Tue, Aug 26, 2014 at 5:13 PM, Peter Hickey wrote:
> Hi Michael,
>
> Thanks for your patience. Here is a self-contained example with comments
> https://gist.github.com/PeteHaitch/fdb66d360446ff96ed4b
>
> Thanks,
> Pete
>
>
> On 27/08/2014,
29/08/2014, at 1:18 PM, Michael Lawrence wrote:
> Added to S4Vectors. Thanks!
>
>
> On Thu, Aug 28, 2014 at 5:04 PM, Peter Hickey wrote:
> Thanks, Michael. Do you think there's a general use case for a replaceROWs,
> NULL method or shall I just specify that in my packag
t;>> CH2LHet CH2RHet CH3LHet CH3RHet CHXHet CHYHet CHUextra
>>>
>>>"dm3""dm3""dm3""dm3""dm3""dm3""dm3"
>>>
>>>[[alternative HTML version del
2014 02:28 PM, Peter Hickey wrote:
>> Just a vote for still allowing for multiple genomes in a Seqinfo object (in
>> a GRanges object). My use case is in bisulfite-sequencing experiments where
>> there is often a spike-in of a lambda phage genome along with the genome of
>
Hi Martin,
The last element of 'x' is never accessed in a call to the internal function
GenomicRanges:::.compare when 'GenomicRanges = TRUE'. The attached patch fixes
this.
Cheers,
Pete
===
--- R/SummarizedExperiment-class.R
graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.19.4 GenomeInfoDb_1.3.6 IRanges_2.1.5
[4] S4Vectors_0.5.3 BiocGenerics_0.13.0
loaded via a namespace (and not attached):
[1] XVector_0.7.1
#-------
led some issues with
>> the behavior of "distanceToNearest" method for GRanges objects.
>> The major issue being that it sometimes returns a Hits
>> object with NAs in it. Val will address this in the next few
>> days.
>>
>> Cheers,
>> H.
>&g
assayNames() helper function in his
bsseq package that is ever so slightly faster. Do others think a general
assayNames() helper function is worth including in GenomicRanges?
Benchmarks at https://gist.github.com/PeteHaitch/346b924e3eca8c3cfade
Thanks,
Pete
------
Hi Marc,
Will a recording be made available? This sounds quite useful, but not quite
"staying up until 2am Australian time" useful :)
Thanks,
Pete
> Message: 5
> Date: Tue, 2 Dec 2014 15:08:08 -0800
> From: Marc Carlson
> To: bioc-devel
> Subject: [Bioc-devel] Google hangout on Wed December
S4Vectors so
using the triple colon should not be necessary (and doing so will
actually trigger a note from R CMD check). Can you provide more
details on why you need this?
Thanks,
H.
On 08/09/2015 09:16 PM, Peter Hickey wrote:
Hi Hervé,
I was having trouble with some devel code of
Sorry, that should say once I made the proposed change to "S4Vectors", not
"IRanges".
On Tue, 11 Aug 2015 8:51 am Peter Hickey wrote:
> Hi Hervé,
>
>
> Hmm, sorry I may have misdiagnosed my problem. I was having problems with
> some code in the bsseq vignett
roblem you're seeing. I think that if you just
> re-install S4Vectors locally (without making the change you proposed)
> the issue will go away. Hopefully...
>
> H.
>
> On 08/10/2015 06:46 PM, Peter Hickey wrote:
> > Sorry, that should say once I made the proposed change
The lengths() function was added in R 3.2 to "get the length of each
element of a list or atomic vector (is.atomic) as an integer or numeric
vector." It seems useful to me to have also a similar method defined for
the S4Vectors::List class (and subclasses). What do others think?
[[alternat
]) is called for all i then it should work on any
>>> object
>>> for which [[ is defined. Note that this is what happens with
>>> base::sapply(), base::mapply(), etc... they all use [[ internally.
>>>
>>> Do you know of any reason why lengths()
See
https://github.com/Bioconductor-mirror/SummarizedExperiment/blob/744eea36e9f8ee4daea00baa7a1d9eea68d957ca/R/SummarizedExperiment0-class.R#L210
I think it should be 'i = assayNames(x)[1]'.
I say it is impossible to trigger because I don't think this method is
ever called since if 'i' is missi
I often find myself with multiple `SE` objects (I'm using `SE` as a
shorthand for the `SummarizedExperiment0` and `RangedSummarizedExeriment`
classes), each with different samples but possibly non-overlapping
features/ranges. Currently, it is difficult to combine these objects;
`rbind()` can only
Sorry, the URL may have been mangled. It's
https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13
<https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13.>
On Thu, 15 Oct 2015 at 12:52 Peter Hickey wrote:
> I often find myself with multiple `SE` objects (I'm using `SE` a
I used to use the git-svn bridge for my GenomicTuples package, which I
develop on GitHub. Several months ago I attempted to switch to the new
method described at
http://bioconductor.org/developers/how-to/git-mirrors/ but made a
complete mess of it. This wasn't so important at the time since I
didn'
some design choices on which I would appreciate some
advice, as discussed in the link.
Thanks,
Pete
On 16 October 2015 at 07:26, Peter Hickey wrote:
> Thanks for your feedback, Martin. I'll have a go at re-implementing
> this and get back to the list next week.
>
> Cheers,
&g
Hi all,
I sometimes want to test whether a GRanges object (or some object with
a GRanges slot, e.g., a SummarizedExperiment object) is (un)sorted.
There is no is.unsorted,GRanges-method or, rather, it defers to
is.unsorted,ANY-method. I'm unsure that deferring to the
is.unsorted,ANY-method is what
hether GenomicRanges
>>> should
>>> have an anyNA method that returns FALSE (and similarly an is.na()
>>> method),
>>> although we have never defined the concept of a "missing range".
>>>
>>> Michael
>>>
>>> On Mon, Nov 2,
ecodeRle(seqnames(x)),
>> start(x), with(x), and S4Vectors:::decodeRle(strand(x)) to the .Call
>> entry point).
>>
>> I'll take your patch if you want to work on this or I can add this
>> to GenomicRanges, let me know. We should probably take this off-list.
>
Hi Leonard,
I'm seeing what I think is a related problem in the devel branch. I
think it derives from some issue with List-based classes. E.g, a
simplified version of your example errors for me (although without
segfault):
> library(IRanges)
# snip - this produces a possibly related warning on my
While on the topic of SummarizedExperiment colnames, the circumstances in
which these are stripped from the assays and overridden by colData is
confusing to me, particularly case 2 below (a warning in case 3 might be
useful too).
> m1 <- matrix(1:10, ncol = 2)
> m2 <- m1
> colnames(m2) <- c("A", "
The Matrix virtual class in the Matrix package seems to mostly work as
an assays element in a SummarizedExperiment. This is especially useful
for data that can be efficiently represented as a sparse matrix, e.g.,
using the dgCMatrix class.
My understanding is that this works because the (concrete
Thanks, Hervé!
On 26/01/2016, Hervé Pagès wrote:
> Hi Pete,
>
> On 01/25/2016 12:32 PM, Peter Hickey wrote:
>> The Matrix virtual class in the Matrix package seems to mostly work as
>> an assays element in a SummarizedExperiment. This is especially useful
>> for d
The assays slot in a SummarizedExperiment object supports elements
with up to 4 dimensions [*]
library(SummarizedExperiment)
makeSE <- function(n) {
assay <- array(1:2^n,
dim = rep(2, n),
dimnames = split(letters[1:(2 * n)], seq_len(n)))
SummarizedExperiment(a
This is mostly directed to Herve and/or Martin, but I'd be interested
in other's input too.
The SummarizedExperiment package defines rbind,Assays-method and
cbind,Assays-method that are called when rbind() or cbind() is called
on a SummarizedExperiment object. In the case of two-dimensional assay
neric.
I quite like arbind() and acbind() as names. I guess these would live in the
SummarizedExperiment package?
Happy to do further work on this but I won't have time until the weekend or
next week.
Cheers,
Pete
On Thu, 3 Mar 2016 at 13:31 Hervé Pagès wrote:
>
> Hi Pete,
>
&g
Wonderful. Thanks, Martin
> in svn at 1.23.5, and in Bioc-devel hopefully after tonight's build.
>
> Martin
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi,
GenomicAlignments::readGAlignmentPairs() can take a while to
(correctly) fail if the `which` parameter contains a "bad" seqlevel.
It'd be great if it failed early in the following scenario (just
experienced).
An example BAM is available from
https://www.dropbox.com/sh/4avqxuqnhlv3r9c/AADqx-Xq
Thanks, Aaron. I implemented a similar workaround, but I think it
would be nice to have in the core Bioconductor implementation. I had a
quick poke around GenomicAlignments::readGAlignmentPairs(), however,
but it looked like I'd have to learn a bit too much about the
underlying Rsamtools::scanBam()
Hi,
The current version of GenomicTuples on the official SVN is 1.5.24
(https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicTuples/DESCRIPTION),
however, the version available via the GitHub mirror is only 1.5.21
(https://github.com/Bioconductor-mirror/GenomicTuples/blob/master/DESC
Typo - github version is 1.5.23
On Mon, 18 Apr 2016 at 09:26 Peter Hickey wrote:
> Hi,
>
> The current version of GenomicTuples on the official SVN is 1.5.24
> (
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicTuples/DESCRIPTION
> ),
> however, the vers
I think this is a recent break. I'm mostly concerned because I need to
use this "broken" functionality in a tutorial for BioC2016 this week
and it would require changes to package internals, not the vignette,
in order to fix this at my end.
library(SummarizedExperiment)
se <- SummarizedExperiment(
h is lagging behind the version that is in svn (1.25.8).
>>> I think this could be what is causing the problem you're reporting
>>> (which I cannot reproduce).
>>>
>>> For now the workaround it to install (or re-install) the latest versions
>>> of S4Vector
I hit an error when calling reduce() on a very big GRanges object
(length = 1170402558). The error was:
Error in .Call2("CompressedIRangesList_reduce", x, drop.empty.ranges, :
_get_new_buflength(): MAX_BUFLENGTH reached
I found MAX_BUFLENGTH is defined in S4Vectors in the file src/AEbufs.c as
The cbind,SummarizedExperiment-method checks that the rowRanges slots
are equal by calling `all(x == x1)`, where x and x1 are GenomicRanges
objects. This can be kind of slow and makes a large, temporary vector
when length(x) is large.
I wrote a fast method to check equality of two GenomicRanges ob
circularity of the underlying sequences e.g. ranges [1, 10] and
> [101, 110] represent the same position on a circular sequence of
> length 100 so should be considered equal. However for 'x == y' and
> 'identicalVals(x, y)', they are not. Something we should address at
I've been toying with the idea of a fixed/constant width Ranges
subclass. The motivation comes from storing DNA methylation data at CH
loci (non-CpG methylation): there are 1.1 billion CH loci in the human
genome, so to store these as a GRanges object requires 2 x 1.1 billion
integer vectors, one f
s fun to remember GPos, which I had forgotten.
>
> On Wed, Nov 23, 2016 at 6:34 PM, Vincent Carey > wrote:
>
> library(GenomicRanges)
> class?GPos
>
> On Wed, Nov 23, 2016 at 6:18 PM, Peter Hickey
> wrote:
>
> I've been toying with the idea of a fixe
l FWRanges class in this case?)
>
> -Ryan
>
> On 11/23/16 8:01 PM, Ryan wrote:
> > Is it possible to allow the width slot of IRanges to be either a
> > normal vector or an Rle?
> >
> >
> > On 11/23/16 6:18 PM, Peter Hickey wrote:
> >> I've bee
Hi,
Recent changes (last few days) that successfully synced from my own GitHub
repo to the BioC SVN and consequent builds don't seem to have propagated to
the BioC GitHub mirror. Anything I should/can be doing to address this?
Thanks,
Pete
[[alternative HTML version deleted]]
__
Sorry, I forgot to say this is the GenomicTuples package
On 22 January 2017 at 10:18, Peter Hickey wrote:
> Hi,
>
> Recent changes (last few days) that successfully synced from my own GitHub
> repo to the BioC SVN and consequent builds don't seem to have propagated to
> th
Thanks, Martin!
On 22 January 2017 at 13:10, Martin Morgan
wrote:
> On 01/22/2017 10:18 AM, Peter Hickey wrote:
>>
>> Hi,
>>
>> Recent changes (last few days) that successfully synced from my own GitHub
>> repo to the BioC SVN and consequent builds don't see
FWIW I've had some success registering Rcpp-based native routines
using Kmisc:::registerFunctions() by Kevin Ushey
(https://cran.r-project.org/web/packages/Kmisc/index.html). Note this
is a non-exported function and from memory it required a little bit of
post-processing, but it got me most of the
Hi Nitesh,
I'm unable to push changes to the GenomicTuples package to the BioC git
host.
$ git push
fatal: remote error: FATAL: W any packages/GenomicTuples nobody DENIED by
fallthru
(or you mis-spelled the reponame)
Following the FAQ (http://bioconductor.org/developers/how-to/git/faq/) I've
run
Doh, I literally spotted that the second I hit send. Sorry for the noise
and thanks!
On Thu, 21 Sep 2017 at 13:55 Turaga, Nitesh
wrote:
> Hi Peter,
>
> If you notice,
>
> On Sep 21, 2017, at 1:53 PM, Peter Hickey wrote:
>
> Hi Nitesh,
>
> I'm unable to p
A partial answer if you are using the 'testthat' framework: you can use
`testthat::skip_on_bioc()` to specify that a test should be skipped if it
is running on the BioC build machines. The test will otherwise be run
(e.g., during local development). There are some other `testthat::skip*()`
function
FYI I also began a project to support an additional backend;
https://github.com/PeteHaitch/matterArray. It's incomplete and may not work
with the current version of DelayedArray (it's ~3 months old and I was
naughtily using some internal functions of DelayedArray). I hope to return
to this soon and
I think that's a good idea, Kylie.
Pete (DelayedMatrixStats developer)
On Thu., 2 Nov. 2017, 6:09 am Kasper Daniel Hansen, <
kasperdanielhan...@gmail.com> wrote:
> I think it makes sense. A lot of sense. Might be useful to involve Henrik
> (matrixStats) as well.
>
> Who are the players, apart fro
As Michael notes, I think the scope here is broader than considering S4
generics for functions in base R. To summarise, I think we would be looking
to have S4 generics for the following:
- All(?) the row*/col* functions in matrixStats (NB: matrixStats uses plain
old functions with no S3 or S4, whi
Thank, Hervé! This is really useful and will help me finish up one such
backend.
Cheers,
Pete
On Wed, 22 Nov 2017 at 18:35 Hervé Pagès wrote:
> Just to let you know that the process of implementing a DelayedArray
> backend is now documented:
>
>
>
> https://github.com/Bioconductor/DelayedArray/
Does `rbind(testhdf, DelayedArray(testdata))` give you what you want?
On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom
wrote:
> Hello,
>
> I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix
> object or DelayedArray object and I am hitting problems. I’m using the
> development ve
Hi Elizabeth,
Aaron and I were hit by this same error message. As a workaround,
installing DelayedArray and HDF5Array from the git(hub) repo fixed the
issue (https://github.com/Bioconductor/HDF5Array/issues/6). But this
needs to be propagated to the versions made available via BiocLite().
Martin:
Thanks, Val. I'm getting an error about "too large files" when I try to
push (see below). Is there a different workflow for pushing an experiment
data package or am I doing something else wrong? bsseqData predates the svn
-> git transition.
Thanks,
Pete
$ git push origin master
Counting objects:
The one-liner on the package landing page describing how to check out
a package from the git repo uses HTTPS rather than ssh, e.g.:
# From https://bioconductor.org/packages/bsseq/
git clone https://git.bioconductor.org/packages/bsseq
However, as a developer we should be using the SSH protocol
(ht
Nitesh, I am still getting the "Error: file larger than 5 Mb" error.
On Sun, 29 Apr 2018 at 09:59 Turaga, Nitesh
wrote:
> Hi Pete,
>
> This should be resolved now.
>
> Best,
>
> Nitesh
> > On Apr 29, 2018, at 9:50 AM, Peter Hickey
> wrote:
> >
&g
sing the HTTPS protocol,
> since they will not have access to download it via SSH ( you need
> permissions to do this).
>
> We always advocate developers to only use SSH though. For everyone else,
> HTTPS is the best option.
>
> Best,
>
> Nitesh
>
> > On Apr 29, 20
29 Apr 2018 at 11:43 Turaga, Nitesh
wrote:
> Can you try with a fresh clone of the repo?
>
> Best,
>
> Nitesh
>
> > On Apr 29, 2018, at 10:21 AM, Peter Hickey
> wrote:
> >
> > Nitesh, I am still getting the "Error: file larger than 5 Mb" error.
&g
ow.
>
> Thanks.
> Val
>
>
>
> On 04/29/2018 09:37 AM, Peter Hickey wrote:
>
> I'm still unable to push large files after a fresh clone. I *am* able to
> push smaller changes (I just tweaked the DESCRIPTION to test this). But I
> get the "Error: file larger t
Tim: As the developer of DelayedMatrixStats (and enthusiastic 'canary down
the coal mine' user-dev of DelayedArray) I'm obviously invested in reducing
the confusion around these packages
I'm going to write some blog posts-cum-vignettes-cum-F1000 around these
issues over the coming weeks, with the
remotes/origin/RELEASE_3_1
remotes/origin/RELEASE_3_2
remotes/origin/RELEASE_3_3
remotes/origin/RELEASE_3_4
remotes/origin/RELEASE_3_5
remotes/origin/RELEASE_3_6
remotes/origin/RELEASE_3_7
remotes/origin/master
$ git log
commit 5eb4c1ebc03fb1d713e873a77570744b94dc7659
Author: Peter Hicke
Successful pushed to both devel and release. Thanks, Nitesh!
On Wed., 2 May 2018, 1:35 pm Turaga, Nitesh,
wrote:
> Try one more time please.
>
> I made some changes after seeing your output.
>
> Best,
>
> Nitesh
>
> > On May 2, 2018, at 1:21 PM, Peter Hickey wrote
erlap in API and
> functionality between 'matrixStats' and 'Matrix' is basically zero(?).
> I think of 'Matrix' a higher-level package. Do my comments above put
> it in a different light? Or are you saying that what's in
> 'matrixStats' should really
Thanks for your work on this, Mike!
On Thu., 23 Aug. 2018, 9:46 pm Mike Smith, wrote:
> Hi all,
>
> I've just submitted updated versions of rhdf5 (2.25.7) and Rhdf5lib (1.3.2)
> to the BioC devel branch. These represent a significant change as the
> underlying version of HDF5 has now changed fr
Great initiative, Mike!
Could these meetings please be recorded?
These will be in the middle of the night in my time zone and I'm sure
others would appreciate being able to view them if they can't make the call.
rOpenSci do something similar with their community calls (
https://ropensci.org/commcal
Hi Tiago,
The following will create a similarly sized subset of the PBMC3k
dataset with the counts in-memory as a sparse matrix:
pbmc3k <- TENxPBMCData::TENxPBMCData("pbmc3k")
mini_pbmc3k <- pbmc3k[1:1700, 1:600]
assay(mini_pbmc3k) <- as(assay(mini_pbmc3k), "dgCMatrix")
Cheers,
Pete
On Mon, 16
I noted the same resource causing the same error for the OSCA books in BIoC
3.20 and Lori said she'll take a look at it tomorrow (only on Slack, sorry:
https://community-bioc.slack.com/archives/CM2CUGBGB/p1719265237989709)
On Tue, 25 Jun 2024 at 12:21, Shian Su via Bioc-devel <
bioc-devel@r-projec
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