In the spirit of 'advent of code', maybe it is better to exploit the features
of the particular language you've chosen? Then the use of factors seems very
relevant.
value_levels <- c("Small", "Medium", "Large")
df <- data.frame(
person = c("Alice", "Bob", "Bob", "Charlie"),
value = facto
Posit employee.
Martin Morgan
From: R-help on behalf of Steven Yen
Date: Thursday, April 6, 2023 at 3:20 PM
To: Uwe Ligges
Cc: R-help Mailing List , Steven T. Yen
Subject: Re: [R] R does not run under latest RStudio
The RStudio list generally does not respond to free version users. I was h
showMethods(LGD, includeDef = TRUE) shows the implementation of all methods on
the LGD generic, and can be a useful fast track to getting an overview of what
is going on.
Martin Morgan
From: R-help on behalf of Ivan Krylov
Date: Thursday, December 8, 2022 at 11:23 AM
To: Christofer Bogaso
You could split the string into letters and figure out which ones are �b�
which(strsplit(x, "")[[1]] == "b")
and then find the difference between each position, �anchoring� at position 0
> diff(c(0, which(strsplit(x, "")[[1]] == "b")))
[1] 2 4 1 6 4
From: R-help on behalf of Evan Cooch
Date:
> strwrap(text)
[1] "What is the best way to split/cut a vector of strings into lines of"
[2] "preferred width? I have come up with a simple solution, albeit naive,"
[3] "as it involves many arithmetic divisions. I have an alternative idea"
[4] "which avoids this problem. But I may miss some existi
One possibility is to make graph a Suggests: dependency, and preface any code
using it (or, e.g., in an .onLoad function) with
if (!requireNamespace("graph", quietly = TRUE))
stop(
"install the Bioconductor 'graph' package using these commands\n\n",
## standard Bioconductor pack
his, as I am still struggling with the inheritance.
The information may be useful, though: it helps in deciding the design
of the data-structures. [Actually, all base-methods should work natively
as well - but to have a solution in any case.]
Sincerely,
Leonard
On 11/17/2
mented is often the [ (single bracket subset) function;
this is relatively complicated to get right, but worth exploring.
I hope that gets you a little further along the road.
Martin Morgan
On 11/16/21, 11:34 PM, "R-help on behalf of Leonard Mada via R-help"
wrote:
Dear List-Members
relevant example at the sqlite command line?
Martin Morgan
On 10/6/21, 2:50 PM, "R-help" wrote:
Thank you Bert, I set up a new thread on
BioStars [1]. So far, I'm a bit
unfamilliar with Bioconductor (but will
hopefully attend a course about it in
November, which I'm kinda hype
#x27;?methods' for accessing help and source code
Martin Morgan
On 5/3/21, 6:34 PM, "R-help on behalf of Therneau, Terry M., Ph.D. via R-help"
wrote:
Is there a complement to the methods function, that will list all the
defined methods for
a class?One solution is
A different approach uses doRedis https://CRAN.R-project.org/package=doRedis
(currently archived, but actively developed) for use with the foreach package,
or RedisParam https://github.com/mtmorgan/RedisParam (not released) for use
with Bioconductor's BiocParallel package.
These use a redis ser
ion path
* DONE (limma)
From: Ayushi Dwivedi
Date: Wednesday, December 23, 2020 at 12:52 AM
To: Martin Morgan
Cc: "r-help@r-project.org" ,
"r-help-requ...@r-project.org"
Subject: Re: [R] error in installing limma
hey.. I used this command to install limma but after
g standard practices documented
on, e.g., https://bioconductor.org/packages/limma to install packages
BiocManager::install("limma")
Martin Morgan
On 12/22/20, 1:11 PM, "R-help on behalf of Ayushi Dwivedi"
wrote:
Good afternoon Sir,
With due respect I want to conv
Lainey wishes to report a bug, so should see ?bug.report. Mail sent to R-core
will be held for moderator approval, and relevant input or ultimate resolution
would not be visible to the wider community; it is not a good place to report
bugs.
Martin Morgan
On 11/16/20, 4:48 PM, "R-he
age took me quickly to your package web site and clear installation
instructions; I do not think use of Bioc packages is a particular barrier to
use.
Martin Morgan
On 10/11/20, 2:52 PM, "R-help on behalf of Søren Højsgaard"
wrote:
Dear all,
My gRbase package imports
ect(), and subset() behave
differently, but for what it's worth subset() can be used to perform these
operations individually
> mytbl %>% subset(, files)
# A tibble: 6 x 1
files
1 a
2 b
3 c
4 d
5 e
6 f
> mytbl %>% subset(grepl("a", files), )
# A tibble: 1 x 2
fi
tend
to keep the plot window (lower right) relatively small, and try to remember to
expand things at the time when the end result is in sight (so to speak;)).
I hope others with more direct experience are not dissuaded by Bert's opinions,
and offer up their own experiences or resource recom
Probably have more success asking on https://support.bioconductor.org.
Martin Morgan
On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha"
wrote:
Hi All,
I have a file list consisting of Chromosome, Start , End & Methylation
Difference in the following f
3 x 4
# Groups: a [2]
a b v1_mean v2_median
1 1 1 1.5 3.5
2 2 2 3 2
3 2 3 4 1
I do not know how performant this would be with data of your size.
Martin Morgan
On 11/8/19, 1:39 PM, "R-help on behalf of Ana Marija
A matrix can be subset by another 2-column matrix, where the first column is
the row index and the second column the column index. So
idx = matrix(c(B, col(B)), ncol = 2)
A[] <- A[idx]
Martin Morgan
On 10/11/19, 6:31 AM, "R-help on behalf of Eric Berger"
wrote:
Here is
Please follow the response to your question on the Bioconductor support site
https://support.bioconductor.org/p/125493/
Martin Morgan
On 10/10/19, 12:23 PM, "R-help on behalf of Ali Siavosh"
wrote:
Hi,
I have installation of R in a server running on redhat 7. I have upgra
Are you remembering to attach the Biobase package to your R session?
> AnnotatedDataFrame()
Error in AnnotatedDataFrame() :
could not find function "AnnotatedDataFrame"
> suppressPackageStartupMessages({ library(Biobase) })
> AnnotatedDataFrame()
An object of class 'AnnotatedDataFrame': none
Bi
installing the package would address this problem.
Martin Morgan
On 1/20/19, 6:58 AM, "R-help on behalf of Duncan Murdoch"
wrote:
On 19/01/2019 8:22 p.m., Peter Waltman wrote:
> I'm trying to install a devel package called gGnome (
> https://github.com/mskilab
Ask on the Bioconductor support site https://support.bioconductor.org
Provide (on the support site) the output of the R commands
library(GEOquery)
sessionInfo()
Also include (copy and paste) the output of the command that fails. I have
> gseEset2 <- getGEO('GSE76896')[[1]]
Found 1 file(s)
sue on the maintainer's github
https://github.com/sneumann/mzR/issues/
this is linked to from the package 'landing page'
https://bioconductor.org/packages/mzR
Martin Morgan
On 06/15/2018 10:49 AM, lejeczek via R-help wrote:
hi guys, just an admin here.
I wonder if anybody see what
ot;b":
An object of class "B"
Slot "y":
numeric(0)
Slot "z":
numeric(0)
> .C(a = .A(x = 1:2), b = .B(y = 2:1, z = 1:2))
An object of class "C"
Slot "a":
An object of class "A"
Slot "x":
[1] 1 2
Slot "b":
An
s and re-thinking the algorithm. Why would one need to
call sapply() millions of times, in a situation where this becomes
rate-limiting? Can the algorithm be re-implemented to avoid this step?
Martin Morgan
Harold
__
R-help@r-project.org mailing list --
is at
http://bioconductor.org/developers/how-to/useDevel/
Martin Morgan
On 01/09/2018 01:32 PM, Sariya, Sanjeev wrote:
Hello R experts:
I need a developer version of a Bioconductor library.
sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Wind
On 12/29/2017 07:00 AM, Pijush Das wrote:
Thank you Michael Dewey.
Can you please send me the email id for Bioconductor.
https://support.bioconductor.org
Make sure you are using packages from a consistent version of Bioconductor
source("https://bioconductor.org/biocLite.R";)
BiocInstaller
On 11/29/2017 05:47 PM, Tóth Dénes wrote:
Hi Martin,
On 11/29/2017 10:46 PM, Martin Morgan wrote:
On 11/29/2017 04:15 PM, Tóth Dénes wrote:
Hi,
A benchmarking study with an additional (data.table-based) solution.
I don't think speed is the right benchmark (I do agree that
correctne
MC
3 07EA001 1962 QMC
4 07EA001 1963 QMC
5 07EA001 1964 QMC
... ... ... ...
20 07EA001 1979 QRC
21 07EA001 1980 QRC
22 07EA001 1981 QRC
23 07EA001 19
On 11/26/2017 08:42 PM, jim holtman wrote:
try this:
##
library(dplyr)
input <- tribble(
~station, ~from, ~to, ~record,
"07EA001" ,1960 , 1960 , "QMS",
"07EA001" , 1961 , 1970 , "QMC",
"07EA001" ,1971 , 1971 , "QMM",
"07EA0
On 09/16/2017 11:29 AM, Rene J Suarez-Soto wrote:
I have not intentionally set R_LIBS_USER. I looked for an Renviron.site
file but did not see it in R/etc or my home directory. The strange part is
that if I print Sud.getenv I see a value for R_LIBS_USER. However, this
directory is not showing und
On 09/15/2017 08:57 AM, Michael Dewey wrote:
In line
On 15/09/2017 13:30, Martin Møller Skarbiniks Pedersen wrote:
On 15 September 2017 at 14:13, Duncan Murdoch
wrote:
On 15/09/2017 8:11 AM, Martin Møller Skarbiniks Pedersen wrote:
Hi,
I am installing a lot of packages to a new R inst
cheOK, quiet, mode to the
download.file() call. 'method' can be determined when you are in
available.packages while debugging; if R says that it is missing, then
it will be assigned, in download.file, to either
getOption("download.file.method") or (if the option is NULL or &quo
ity issue, or perhaps an
issue with the CRAN mirror you're using. Can you debug on your end, e.g,.
options(error=recover)
install.packages("withr")
...
then select the 'frame' where the error occurs, look around
ls()
find the value of 'dest', and e.g., try
Rsamtools and GenomicAlignments are Bioconductor packages so ask on the
Bioconductor support site
https://support.bioconductor.org
You cannot rename the seqlevels in the bam file; you could rename the
seqlevels in the object(s) you have created from the bam file.
Martin
On 02/14/2017 09:1
On 02/01/2017 02:46 PM, Ramiro Barrantes wrote:
Hello,
I have a function that applies to an S4 object which contains a slot called
@analysis:
function calculation(myObject) {
tmp <- myObjects@analysis
result <- ...operations on analysis...
return result
}
I am writing a unit test for th
On 10/23/2016 10:13 PM, Yogesh Gupta wrote:
Dear All,
I am getting error in DESeq installation in R.
package ‘DESeq’ is not available (for R version 3.3.1)
source("http://www.Bioconductor.org/biocLite.R";)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
biocLite("BiocUpgr
On 09/28/2016 02:53 PM, Hervé Pagès wrote:
Hi,
I'm surprised nobody suggested split(). Splitting the data.frame
upfront is faster than repeatedly subsetting it:
tmp <- data.frame(id = rep(1:2, each = 10), foo = rnorm(20))
idList <- unique(tmp$id)
system.time(for (i in idList) tmp
/doc/manuals/r-release/R-exts.html#Using-Makevars
Martin Morgan
PS I tested the ssame behaviour with various version of R from R/2.15 to
R/3.3
best regards
Eric
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
http
On 08/05/2016 12:07 PM, Guido Kraemer wrote:
Hi everyone,
we are running R on a Linux Cluster with several R versions installed in
parallel.
If I run:
library(parallel)
cl <- makePSOCKcluster(
rep('nodeX', 24),
homogeneous = FALSE,
rscript = '/usr/local/apps/R/R-3.2.2/bin/Rscript'
)
fr
ate a vector
rep(seq_along(d), lengths(d)), and split it into groups defined by f
f = factor(unlist(d, use.names=FALSE), levels=queries)
split(rep(seq_along(d), lengths(d)), f)
Martin Morgan
Thanks in advance !!
Tanvir Ahamed
Göteborg, Sweden | mashra.
packages, e.g.,
https://cran.r-project.org/bin/linux/debian/)
Martin Morgan
Jakub
On 13. May 2016, at 11:31, Martin Morgan
wrote:
On 05/12/2016 10:25 PM, Alba Pompeo wrote:
Martin Morgan, I tried an HTTP mirror and it worked. What could
be the problem and how to fix? Also, should I ignore t
On 05/12/2016 10:25 PM, Alba Pompeo wrote:
Martin Morgan, I tried an HTTP mirror and it worked.
What could be the problem and how to fix?
Also, should I ignore the warning about ignoring environment value of R_HOME?
It depends on why you set the value in your environment in the first
place
On 05/12/2016 10:25 PM, Alba Pompeo wrote:
Martin Morgan, I tried an HTTP mirror and it worked.
What could be the problem and how to fix?
The problem is in the warning message
1: In download.file(url, destfile = f, quiet = TRUE) :
URL 'https://cran.r-project.org/CRAN_mirrors.csv
ave any success when choosing a non-https mirror, #28 in your
screenshot?
Martin Morgan
Thanks a lot.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting gui
rived
classes corresponding to stateless or stateful conditions
Base = setClass("Base"); A = setClass("A", contains="Base"); A()
Martin Morgan
Thanks.
Ross Boylan
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and
rtunity for gain (compared to grepl) on
non-Windows
> system.time(res2 <- pvec(seq_along(grams), function(i)
grepl("^91", grams[i]), mc.cores=8))
user system elapsed
24.996 1.709 3.974
> identical(res0, res2)
[[1]] TRUE
I think anything else would require pre-proce
efault is
> stats:::coef.default
function (object, ...)
object$coefficients
Maybe fail on use, rather than trying to guess up-front that the object
is fully appropriate?
Martin Morgan
Right now, I'm contemplating this:
zz1 < - try(coef(zz))
if (inherits(zz1, "try-error"
Use a local environment to as a place to store state. Update with <<-
and resolve symbol references through lexical scope E.g.,
persist <- local({
last <- NULL# initialize
function(value) {
if (!missing(value))
last <<- value #
On 03/22/2016 12:44 AM, Omar André Gonzáles Díaz wrote:
Hi,I have a DF with a column with "html", like this:
https://ad.doubleclick.net/ddm/trackimp/N344006.1960500FACEBOOKAD/B9589414.130145906;dc_trk_aid=303019819;dc_trk_cid=69763238;ord=[timestamp];dc_lat=;dc_rdid=;tag_for_child_directed_tre
On 03/14/2016 06:39 PM, Mohammad Tanvir Ahamed via R-help wrote:
Hi, i got an error while i am running a big data. Error has explained
by the following sample sample
This is an error in the package, and should be reported to the
maintainer. Discover the maintainer with the command
main
a") if (missing(by)) by
> f()
[1] "sea"
which is the case for seq.default
> args(seq.default)
function (from = 1, to = 1, by = ((to - from)/(length.out - 1)),
length.out = NULL, along.with = NULL, ...)
Martin Morgan
--
Computational Biology / Fred Hutchinson Cancer Re
On 08/05/2015 11:52 AM, Greg Donald wrote:
I'm using RCurl with postForm() to post to a URL that responds with a
PDF. I cannot figure out how to write the resulting PDF data to a
file without corruption.
result = postForm(url, binary=TRUE)
Both this:
capture.output(result, file='/tmp/export.p
On 08/05/2015 10:08 AM, Jeff Newmiller wrote:
New versions are released when they are ready. This is volunteer-driven
software.
From https://developer.r-project.org/ :
The overall release schedule is to have annual x.y.0 releases in Spring, with
patch releases happening on an as-needed basis
, maybe you can take out the
middleman ?
Martin Morgan
But after doing
make check
I get
comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ...make[3]: *** [d-p-q-r-tests.Rout]
Fehler 1
make[3]: Verzeichn
On 06/05/2015 10:52 AM, Martin Maechler wrote:
Christophe Genolini
on Fri, 5 Jun 2015 00:36:42 -0700 writes:
> Hi all,
> There is a compatibility issue between the package 'lme4' and my package
> 'kml'. I define the "[" operator. It works just fine in my package (1).
If I
On 06/04/2015 10:08 AM, cgenolin wrote:
Hi the list,
I have a variable y that is either NA or some S4 object. I would like to
know in which case I am, but it seems taht is.na does not work with S4
object, I get a warnings:
--- 8<
setClass("myClass",slots=c(x="numeric"))
if(runif(1)
On 05/28/2015 08:21 AM, Duncan Murdoch wrote:
On 28/05/2015 6:10 AM, Claire Rioualen wrote:
Hello,
I can't seem to install R packages, since it seemed there were some
permission problems I "chmoded" /usr/share/R/ and /usr/lib/R/. However,
there are still errors in the process. Here's my config:
incebuffalo.com/2012/03/12/23andme-gwascat.html which is a
little dated and maybe not relevant to your question.
A little tangentially, see also https://support.bioconductor.org/p/67444/
Martin Morgan
On 18 May 2015 at 03:04, Bert Gunter wrote:
(No response necessary)
What struck me abou
e message produces.
There is a 'worked example' at
http://bioconductor.org/developers/how-to/c-debugging/#case-study
Of course this might lead to nothing, and then you'll be back to your original
question about using gctorture or other strategies.
Martin Morgan
I have already underta
On 03/16/2015 05:05 PM, Saptarshi Guha wrote:
Example was complicated, but here is a simpler form
continueIfTrue <- function(mm=return()){
eval(mm)
}
telemStats <- function(){
y <- substitute(return())
continueIfTrue(y)
print("I would not like this message to be printed")
}
t
On 03/11/2015 01:36 AM, Søren Højsgaard wrote:
Dear all,
My package 'gRbase' uses three packages from Bioconductor and these are not
automatically installed when gRbase is installed. My instructions (on the
package webpage) to users are therefore to run:
Treat Bioconductor packages as any o
On 03/05/2015 01:21 AM, Zaynab Mousavian wrote:
Hi all,
I have tried to install GO.db package in R, but the following error is
please ask questions about Bioconductor packages on the Bioconductor support
forum https://support.bioconductor.org. Please also review answers to your
question on B
On 01/16/2015 10:21 PM, Mike Miller wrote:
First, a very easy question: What is the difference between using
what="character" and what=character() in scan()? What is the reason for the
character() syntax?
I am working with some character vectors that are up to about 27.5 million
elements long.
e first place (as a matrix of appropriate type, rather than
data.frame, so the entire coercion is irrelevant). If faced with a data.frame
with specific columns to coerce I would use the approach
cidx <- sapply(df, is.character) # index of columns to coerce
df[cidx] <- lap
at least when the url has been seen
'recently'), then configure R to use a local mirror from
http://bioconductor.org/about/mirrors/, e.g.,
chooseBioCmirror()
Martin Morgan
Bioconductor
AlexG
__
R-help@r-project.org mailing list -- To
On 12/06/2014 02:53 PM, ce wrote:
Dear all,
Let's say I have this script , below. tryCatch indeed catches the error but
exists, I want function to continue and stay in the loop. I found very
examples of withRestarts on internet to figure it out. Could you help me how to
do it ?
myfunc <-
nimal, self-contained, reproducible code.
--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.c
think this is appropriate for the R-devel mailing list
http://www.r-project.org/posting-guide.html#which_list)
Martin Morgan
Best,
Charles
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building
...) {}
setGeneric("foo", function(x, ...) standardGeneric("foo"))
?
Martin Morgan
Thanks,
Glenn
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/
ready seen increased (quantifiable)
and broader (subjective) participation from the Bioconductor community. I'd be
happy to make support site usage data available, and am interested in
collaborating in an academically well-founded analysis of this data; any
interested parties please feel
ot; not being valid or,
worse, a hang
from an input command waiting for the user to type something into standard input
(because
scan() and others treat file="" the same as scan=stdin()).
Bill Dunlap
TIBCO Software
wdunlap tibco.com <http://tibco.com>
On Mon, Nov 24, 2014 at 10:36 AM, Ma
On 11/24/2014 06:18 AM, Luigi wrote:
Dear all,
I would like to use the R's Bioconductor package flowCore to do flow cytometry
Please address questions about Bioconductor packages to the Bioconductor support
site
https://support.bioconductor.org
and...
analysis.
I generated a FCS file us
On 11/16/2014 10:25 AM, jarod...@libero.it wrote:
Dear all!,
I use this code:
dds <- DESeq(ddHTSeq)
res <-results(dds)
#reporting
library(ReportingTools)
library("org.Hs.eg.db")
des2Report <- HTMLReport(shortName ='RNAseq_analysis_DESeq2.html',title ='RNA-seq
analysis of differential expressi
ung there. So things spawned anyway, which is progress. I'm just not
sure is that expected behavior for parSupply or not.
Jim
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wednesday, September 03, 2014 5:08 PM
To: Leek, Jim; r-help@r-project.org
Subject
On 09/03/2014 03:25 PM, Jim Leek wrote:
I'm a programmer at a high-performance computing center. I'm not very
familiar with R, but I have used MPI from C, C++, and Python. I have to run
an R code provided by a guy who knows R, but not MPI. So, this fellow used
the R snow library to parallelize
On 08/28/2014 11:47 PM, my1stbox wrote:
Hi all,
First, I carried out GO enrichment to predicted/validated target genes of those
miRNA using GOstats package. Then I find myself in a dead end. So what is the
good practice? Is it possible to directly do GO enrichment to miRNAs? Are they
included
A warn-off on R-help seems entirely warranted. Good to see that
Martin Morgan is taking the issue very seriously in his post below.
As a non-BioC user using BioC packages I've always wondered why the standard R
functionality isn't enough. Can someone, please, tell me why 'biocLite
This would be very bad and certainly unintended if it were the responsibility of
biocLite. Can we communicate off-list about this? In particular can you report
noquote(readLines("http://bioconductor.org/biocLite.R";))
?
Martin Morgan
On 05/17/2014 10:16 PM, Juergen Rose wrote:
On 04/09/2014 07:23 AM, Raghu wrote:
I am unable to install flowDensity package from bioconductor in R version 3.0 or
3.1.
did anyone have the same problems with this.
Please ask questions about Bioconductor packages on the Bioconductor mailing
list
http://bioconductor.org/help/mailing-list
Hi Ross --
On 01/23/2014 05:53 PM, Ross Boylan wrote:
[Apologies if a duplicate; we are having mail problems.]
I am trying to understand the circumstances under which R makes a copy
of an object, as opposed to simply referring to it. I'm talking about
what goes on under the hood, not the user
Hi Nancy --
cummeRbund is a Bioconductor package so please ask questions about it on the
Bioconductor mailing list.
http://bioconductor.org/help/mailing-list/mailform/
Be sure to include the maintainer packageDescription("cummeRbund")$Maintainer in
the email.
You have the 'latest' versio
On 11/09/2013 11:31 PM, Hadley Wickham wrote:
Modelling a mutable entity, i.e. an account, is really a perfect
example of when to use reference classes. You might find the examples
on http://adv-r.had.co.nz/OO-essentials.html give you a better feel
for the strengths and weaknesses of R's differe
the way S4 classes work.
If instead of a single account you modelled 'Accounts', i.e., all accounts, then
updating 1000 account id's would only make one copy, whereas if you model each
account separately this would require 1000 copies.
Martin
thanks..
On Sat, Nov 9, 2013
Depending on implementation, updating S3 objects could as easily trigger copies;
this is a fact of life in R. Mitigate by modelling objects in a vector
(column)-oriented approach rather than the row-oriented paradigm of Java / C++ /
etc.
Martin Morgan
2) Documentation. It has been really ha
On 11/09/2013 06:31 AM, daniel schnaider wrote:
It is my first time programming with S4 and I can't get the setter fuction
to actually change the value of the slot created by the constructor.
I guess it has to do with local copy, global copy, etc. of the variable -
but, I could't find anything r
On 11/01/2013 08:22 AM, Magnus Thor Torfason wrote:
Sure,
I was attempting to be concise and boiling it down to what I saw as the root
issue, but you are right, I could have taken it a step further. So here goes.
I have a set of around around 20M string pairs. A given string (say, A) can
either
On 10/17/2013 08:54 AM, Michael Meyer wrote:
Suppose you have a base class "Base" which implements a function "Base::F"
which works in most contexts but not in the context of "ComplicatedDerived"
class
where some preparation has to happen before this very same function can be
called.
You woul
On 10/16/2013 06:32 AM, John linux-user wrote:
Hello everyone,
I am wondering how to simply merge two GRanges objects by range field and add
the value by additional vector. For example, I have two objects below
Hi -- GRanges is from a Bioconductor package, so please ask on the Bioconductor
On 10/02/2013 09:28 AM, Asis Hallab wrote:
Dear Bioconductor Experts,
This will be responded to on the Bioconductor mailing list; please address any
follow-ups there.
http://bioconductor.org/help/mailing-list/
Martin
thank you for providing such a useful tool-set.
I have a question reg
On 08/24/2013 04:50 AM, Robin Mjelle wrote:
after updating R and edgeR I lost the annotations in the final
Diff.Expressed matrix (toptags) when running the edgeR pipeline. How do I
get the row.names from the data matrix into the topTag-matrix?
data <- read.table("KO_and_WT_Summary_miRNA_Expressi
ding the code? Where can I find the source code?
Best
Simon
On Aug 8, 2013, at 10:00 PM, Martin Morgan wrote:
On 08/04/2013 02:13 AM, Simon Zehnder wrote:
So, I found a solution: First in the "initialize" method of class C coerce
the C object into a B object. Then call the next method
On 08/04/2013 02:13 AM, Simon Zehnder wrote:
So, I found a solution: First in the "initialize" method of class C coerce
the C object into a B object. Then call the next method in the list with the
B class object. Now, in the "initialize" method of class B the object is a B
object and the respecti
On 07/23/2013 09:59 AM, Simon Zehnder wrote:
Hi David,
thanks for the reply. You are right. Using the %in% is more stable and I gonna
change my code.
you said you were you were using S4 classes. S4 classes do not report vectors of
length != 1, from ?class
For objects which have a form
On 07/18/2013 03:47 AM, Simon Zehnder wrote:
Hi Christopher,
I think, that "save" is no generic function like "plot", "show", etc. So at
first you have to determine a generic.
setGeneric("save", function(x, file_Path) standardGeneric("save"))
The implementation offered by Christofer shows wr
On 07/16/2013 06:36 AM, Steve Creamer wrote:
Dear AllI am really struggling with oo in R. Trying to set attributes of
the base class in a derived class method but the slot is only populated in
the method itself, not when I try to print out the object from the console.
Code is
library(RODBC)
On 07/15/2013 06:25 AM, Duncan Murdoch wrote:
On 15/07/2013 8:49 AM, Andreas Leha wrote:
Hi Helios,
"Helios de Rosario" writes:
>> Hi all,
>>
>> several packages print messages during loading. How do I avoid to
> see
>> them when the packages are in the defaultPackages?
>>
>> Here is an exam
lly I want all the GO BP annotations for my organism and from them I
> want to retain only those annotations which annotate less than a specified
> number of genes. (say <1000 genes)
>
> I hope I have put it clearly.
>
> sorry again.
>
> Thanks!
>
>
> On S
1 - 100 of 542 matches
Mail list logo
